Data Collection

Four high-resolution, boat-based mapping surveys were done across broad areas of the Delta (fig. 1) in spring 2018, 2020, 2021, and 2022. Each survey was completed over 3–4 consecutive days (table 2).

The methods for each boat-based, high-resolution mapping survey followed the approach described by Downing and others (2016), Fichot and others (2016), Kimmerer and others (2019), Bergamaschi and others (2020), Stumpner and others (2020), and Richardson and others (2023c). Detailed methods for each survey are provided with their associated data: Bergamaschi and others (2020) for 2018 surveys, O’Donnell and others (2023) for 2020 and 2021 surveys, and O’Donnell and others (2024) for 2022 surveys. Briefly, water was continuously pumped from about 1-meter (m) depth to a flow-through system comprised of in situ instruments (including those listed in table 3, among others) deployed on a 26-foot research vessel. The research vessel navigated throughout the Delta at speeds as much as 30 knots (15.4 meters per second), while instruments recorded data at a frequency of 1 unique measurement per second.

During each survey, the research vessel stopped at about 30 fixed stations (fig. 1; table 4) to collect a suite of discrete samples analyzed for concentrations of NH₄⁺, NO₃⁻, nitrite (NO₂⁻), phosphate (PO₄³⁻), dissolved organic carbon (DOC), and chlorophyll a captured on a 0.2-micrometer (µm) filter, as well as phytoplankton enumerated according to traditional methods as described by Bergamaschi and others (2020). Additionally, discrete samples were collected about every 2 mi while underway for additional nutrient analysis. In 2018, these additional samples were analyzed for PO₄³⁻ only, whereas they were analyzed for PO₄³⁻, NH₄⁺, NO₃⁻ + NO₂⁻, and NO₂⁻ during the other 3 years. During some surveys, discrete samples collected at fixed stations also were analyzed for picophytoplankton, optical properties of dissolved organic matter, the fraction of larger celled chlorophyll a containing organisms captured on a 5-micrometer filter, cyanotoxins, suspended sediment concentration and composition, and other constituents; however, those data are not included in this report.

Chlorophyll fluorescence (reported in micrograms per liter [µg/L] of chlorophyll) is an in situ measurement used as a proxy for chlorophyll concentration. Although several different chlorophyll fluorometers were deployed during the mapping surveys, we report chlorophyll data collected by the bbe Molaenke FluoroProbe (bbe Moldaenke, Germany), which provides a value for total chlorophyll fluorescence in units of µg/L and attributes that fluorescence to four groups of phytoplankton: (1) diatoms; (2) cryptophytes; (3) cyanobacteria; and (4) green algae (Beutler and others, 2002; Harrison and others, 2018; Delascagigas, 2021). In addition to the high-resolution chlorophyll data, discrete samples were collected at each fixed station (fig. 1; table 4) for phytoplankton enumeration by microscopy. Generally, phytoplankton groupings commonly enumerated in samples from the Delta can be matched to FluoroProbe channels based on primary pigmentation (table 5).

Data Processing

Data (Bergamaschi and others, 2020; O’Donnell and others, 2023, 2024) were median filtered with a 20-second moving window to remove outliers, except for the NH₄⁺ data. Discrete NH₄⁺ data were used to validate data from the continuous ammonium flow-through analyzer (Richardson and others, 2023c), discrete NO₃⁻ + NO₂⁻ data were used to calibrate data from the SUNA V2 NO₃⁻ sensor, and discrete DOC data were regressed against the in situ dissolved organic matter fluorescence (fDOM) data to model DOC concentrations (Bergamaschi and others, 2020; O’Donnell and others, 2023, 2024).

Although the exact temporal (date and time) and spatial (latitude and longitude) attributes of the high-resolution data generated during the surveys are relevant because they can be related to specific hydroclimate data (for example, point in the tide or time of day) and specific landscape-scale factors (for example, geomorphology or aquatic vegetation), these exact attributes make it difficult to compare data across surveys. Likewise, different routes were taken during each survey, and some locations were mapped twice in 1 day (for example, dead-end sloughs) or mapped on more than 1 day because of overlapping transects. Thus, to facilitate comparison among dates, data were geo-rectified in a method that minimized effects of disparate data density. Briefly, the GeoPandas software library (Jordahl and others, 2020) in Python was used to assign the median-filtered data attributes from Delta-wide polygon shapefiles that are spaced at about 150-m intervals, including a polygon identifier (ID; identifier unique to each 150-m length shapefile) and geospatial information, like the regions presented on figure 2 and finer resolution metadata, like slough, river reach, bay, and so on. Polygon identification numbers were used to aggregate data and obtain summary statistics. To make contour maps, raster images were created using these data with Environmental Systems Research Institute, Inc. (Esri) ArcGIS Pro version 2.2.1 Spline with Barriers tool (based on Terzopoulos and Witkin [1988]; Esri, Inc., Redlands, California). The Focal Statistics tool in ArcGIS Pro (Esri, Inc., Redlands, California) was then used to smooth the raster, and data were interpolated (where missing) with the ArcGIS Extract Multi Values to Points tool (Esri, Inc., Redlands, California). The Contour tool in ArcGIS Pro (Esri, Inc., Redlands, California) was used to convert the smoothed and interpolated rasters to vectors, and then the National Hydrography Dataset (U.S. Geological Survey, 2016) was used to clip the polygons into the final format included in this report.

The surveys were done across nine broadly defined hydrodynamic zones of the Delta (fig. 2; Jabusch and others, 2016; Bergamaschi and others, 2024; Brown and others, 2024). The three tidal transition zones represent locations where river flow transitions from flowing toward the sea (gravity-driven) to being mostly tidally driven. Tidal zones are locations where the major hydrologic effect is tidal forcing. The Suisun Bay zone encompasses the brackish zone, which connects the Delta to the San Francisco Bay.

Routes taken by the research vessel were similar, but not identical, across surveys (fig. 3; Bergamaschi and others, 2020; O’Donnell and others, 2023, 2024). Only data collected in the same location (for example, within 150 m of each other) of all four spring surveys (fig. 4) are presented in the box plots presented in this report). Data were separated by zones, defined on figure 2, and shown in box plots to use as companions to the provided Delta-wide contour maps. The contour maps are for exploring gradients across the Delta during the same general period (for example, spring) and for visual reference of differences across study periods.

Water-Year Type

The Sacramento and San Joaquin Valley Water Year Hydrologic Classification Index—commonly referred to as “water-year type”—is calculated by the California Department of Water Resources (CDWR) for the Sacramento and San Joaquin River Basins based on modeled, unimpaired water runoff (California Department of Water Resources, 2024a). Unimpaired water runoff is defined as the natural water production of a river basin unaltered by upstream diversions, storage, and export of water to or import of water from other basins. The index categorizes each water year (October 1 to September 30) as one of the following: wet, above normal, below normal, dry, or critical.

For the Sacramento River Basin, water year 2018 is defined as “below normal,” 2020 is defined as “dry,” and water years 2021 and 2022 are defined as “critical” (fig. 5).

To demonstrate how the outflow can differ by water year, the cumulative sum of Delta outflow at Chipps Island (fig. 2) in million cubic feet per second (Mft³/s) by water year is shown on figure 5 for water years 2014–22. A stark difference in cumulative outflow is evident by water-year type. Water years with higher cumulative outflow are associated with lower water residence time, lower salinity in the estuary, and higher dilution of some nutrient inputs, like wastewater treatment plant effluent, but can also increase upstream nutrient loading in the Sacramento River due to increased runoff. Previous water-year types may affect subsequent water years, particularly during the spring surveys; the 2018 and 2020 surveys were preceded by wet water years.

Delta Outflow

Delta outflow is a measure of the net amount of freshwater that passes through the Delta into San Francisco Bay and is determined by a water balance (combination of inflows and exports; California Department of Water Resources, 2024b). The average daily measurement is an estimate of net outflow at Chipps Island, a location at the confluence of all major tributaries to the estuary (fig. 2). The data shown on figure 6 are the daily average Delta outflow and are used to determine the cumulative sums shown on figure 5. The vertical lines on figure 6 indicate when the four spring surveys were completed. The May 2018 survey took place after major flows and captured the highest flows of the four surveys. In context, however, the Delta outflow was still relatively low during the May 2018 survey compared to much of the following year (water year 2019).

The mean Delta outflow ranged from 4,955 to 9,738 cubic feet per second (ft³/s) during the four spring surveys, decreasing each survey (fig. 6; table 6). The lower flows in the later surveys are associated with higher water residence time and less constituent dilution, especially compared to the initial 2018 survey. Longer water residence time allows more time for biogeochemical transformations, more time for phytoplankton growth, and allows slower growing phytoplankton species to compete with faster growing species (Smith and others, 2014).

Export:Outflow Ratio

Relating Delta exports to Delta outflow can give insight into Delta hydrodynamic conditions. Delta exports are the sum of water diverted from the Central Valley Project pumping at Tracy Pumping Plant, the Contra Costa Water District diversions at Middle River, Rock Slough and Old River, the North Bay aqueduct and State Water Project exports, including the Harvey O. Banks Pumping Plant or Clifton Court Forebay intake (fig. 2; California Department of Water Resources, 2021). The ratio of water diverted from the system to that flowing into the San Francisco Bay, referred to as the “export:outflow ratio,” approaches zero when water exports are small relative to water outflow to the ocean (California Department of Water Resources, 2021). A higher export-to-outflow ratio reflects that a higher proportion of freshwater inflows to the Delta are diverted for use within the Delta or elsewhere, rather than flowing out to the bay. Across an annual timescale, the ratio typically is lowest in late spring when winter runoff and reservoir outflow are greatest and during storms, which are more typical in the late fall and winter. There is a steady increase in the ratio in June relative to May across most years and is consistent with pumping requirements for agriculture. The average daily export:outflow ratio for each spring survey was 0.16, 0.23, 0.11, and 0.16, respectively (table 6). The 2020 survey, which was done in June rather than May (delayed due to the coronavirus disease 2019 [COVID-19] pandemic), reported a higher average export:outflow ratio compared to the other three surveys.

Because the average Delta outflow measurement in 2022 was about 50 percent of what it was in 2018, yet average export:outflow ratios for the 2 years were equal, this means Delta exports also decreased by about 50 percent in 2022 compared to 2018. This result can be attributed to the ongoing drought. The average export:outflow ratio was lowest during the 2021 survey, although Delta outflow was second lowest amongst the surveys at 5,308 ft³/s (table 6). The pumping was likely lowest during the 2021 survey because of the lack of rain that water year and subsequent limits on exports (figs. 5–6).

X₂ Position

Another metric that provides information about water-quality conditions in the Delta is the position of X₂, which is defined as the distance from the Golden Gate Bridge to the point upstream where bottom salinity is 2 parts per thousand (Jassby and others, 1995). For example, target X₂ positions in October after an above-normal water year are less than or equal to 74 kilometers (km; Crader and others, 2010). The Bureau of Reclamation and CDWR are tasked with managing X₂ based on Action 4 of the U.S. Fish and Wildlife Service Reasonable and Prudent Alternative regulations designed to protect aquatic life in the Delta (National Research Council, 2010). This task is achieved by managing both reservoir releases to the Delta and exports out of the Delta. X₂ positions farther upstream reflect lower freshwater flows from the Delta, allowing saline water from the San Francisco Bay to move farther upstream and can indicate that encroaching brackish water is reducing the area of freshwater habitats where productivity by phytoplankton is typically higher.

The average X₂ position during the period of mapping in May 2020, 2021, and 2022 was farther upstream (78, 84, and 83 km, respectively) relative to May 2018 (70 km) and was consistent, given that 2018 was a wetter year based on the water year index. The X₂ position was farther upstream in the later years compared to the spring 2018 survey, which indicates the species composition between the X₂ positions may differ because the area of freshwater phytoplankton habitat may have been reduced with each survey and likewise the habitat for euryhaline phytoplankton may broaden. Because the increase in X₂ through surveys is directly related to worsening drought conditions, we will primarily focus on the effects of droughts in this report instead of framing by effects of X₂.

Delta Cross Channel Status

Water resource management affects water flow and mixing in the Delta. For example, when open, the Delta Cross Channel (DCC) allows Sacramento River water to flow to the Mokelumne River and into the San Joaquin River via Snodgrass Slough (fig. 2). Because EchoWater Facility effluent enters the Sacramento River upstream from the DCC when the gates are open, higher nutrient-containing water is diverted into the northern end of the Mokelumne system tidal transition zone (fig. 2). As such, DCC operations must be considered in our comparison among survey dates. Each of the four spring mapping surveys described in this report were done when the DCC was closed (Bureau of Reclamation, 2022); however, before the spring 2020 survey (June 8–11), the DCC had been opened from May 22 to 26, May 30 to June 1, and June 6 to 8. In 2021, a series of DCC gate operation tests were done 6 days before the spring survey (May 11–14), which consisted of three brief openings (each about 30 minutes) pulsing Sacramento River water into Snodgrass Slough (Bureau of Reclamation, 2022).

Drought Barrier Status

One distinct difference during the spring 2022 survey was the presence of the emergency drought salinity barrier near the mouth of the west False River (fig. 2). This barrier is only put in place during extreme drought conditions. The purpose of this barrier is to limit salinity intrusion into the central Delta to protect the quality of water exported from the Delta for drinking water and irrigation (Kimmerer and others, 2019). The placement of the barrier alters flow by decreasing tidal dispersion into the Franks Tract State Recreation Area (fig. 2).

EchoWater Facility Status

Effluent inflow to the Sacramento River from the EchoWater Facility is identified as one of the main drivers of nutrient concentrations in the Delta, particularly during low flow periods when upstream nutrient concentrations are low and effluent inputs are less diluted (Senn and others, 2020). Although the total amount (loading) of nutrients entering the Delta from the EchoWater Facility is a function of effluent nutrient concentrations and effluent flow (concentration and volume), the resulting riverine concentration is affected by the ratio of effluent flow to river flow (dilution). Typical EchoWater Facility effluent volumes comprise about 1–3 percent of the total Sacramento River flow during spring conditions; however, during low flow periods when river reversals occur in this part of the river, effluent contributions can increase to 6 percent for brief periods (typically less than 1 hour), resulting in parcels of water with higher concentrations of effluent-derived nutrients in the river (O’Donnell, 2014; Kraus and others, 2017a). Thus, lower Sacramento River flows associated with drought periods (for example, 2020 and onward within this report) had higher percentages of EchoWater Facility effluent in the Sacramento River, as well as longer water residence times.

Because there were key changes to EchoWater Facility effluent nutrient concentrations and forms between the spring surveys, the percentage of effluent in relation to flow conditions is not the only key factor to consider regarding EchoWater Facility operations. Between the spring 2018 and 2020 surveys, EchoWater Facility effluent had a notable increase in NO₃⁻ concentration after the implementation of the Nitrifying Sidestream Treatment project (fig. 7). BNR Phase 1 began in fall 2020, and Phase 2 was implemented just before the spring 2021 survey. The final spring 2022 survey was completed just over 1 year after the BNR Phase 2 upgrade implementation. Effluent nitrogen concentration data (fig. 7) indicated that EchoWater Facility upgrades effectively reduced NH₄⁺ effluent concentrations from about 1,500–2,500 micromolars (µM; about 20–35 milligrams per liter [mg/L] of nitrogen) to near zero (the reporting limit for effluent NH₄⁺ concentration is 35.7 µM, equivalent to 0.5 mg/L of nitrogen) and increased NO₃⁻ concentrations from near zero (the reporting limit for effluent NO₃⁻ concentration is 7.1 µM, equivalent to 0.1 mg/L of nitrogen) to about 500 µM (about 7 mg/L of nitrogen); as a result, effluent DIN (NH₄⁺+NO₃⁻+NO₂⁻) was reduced by more than 80 percent. In addition to decreases in effluent inorganic nitrogen inputs, the upgrade also resulted in lower phosphorus (P) concentrations, both for PO₄³⁻ and total P (fig. 8).

Ammonium

Main findings are listed here:

Concentrations of NH₄⁺ across the study area ranged from a high near 57 μM in the north Delta tidal transition zone during the 2018 survey to negligible (near zero) concentrations in all zones during the May 2022 survey (figs. 9–10; tables 1.1–1.9). In the segment of the Sacramento River, above the EchoWater Facility, which serves as a control zone where nutrients and water quality are unaffected by EchoWater Facility effluent discharge, median NH₄⁺ concentrations were 0.3, 0.8 1.9, and 0.4 μM during the 2018, 2020, 2021, and 2022 spring surveys, respectively (fig. 9; table 1.1). These concentrations indicated no decrease through time that might confound the effects of the upgrade. It is worth noting that during the 2018, 2021, and 2022 surveys, flows were reversing at Freeport, requiring the EchoWater Facility to halt effluent flows during peak flood tide periods to meet its permit requirements. Nevertheless, when river flows reverse, effluent-containing river water can be transported upstream into this zone, which explains the high outlier NH₄⁺ concentrations observed in the Sacramento River above the EchoWater Facility in 2018 and 2020 (fig. 9).

In the main stem of the Sacramento River, NH₄⁺ concentrations immediately below the EchoWater Facility remained elevated during the 2021 spring survey, even though it was completed several days after the BNR Phase 2 upgrade was fully implemented (fig. 7). This lag may represent a reservoir of effluent-derived NH₄⁺ that was retained in this river reach (for example, due to incomplete flushing or sediment storage) and was released over time after the upgrade (Senn and others, 2020). It seems this reservoir was depleted by the spring 2022 survey.

The highest NH₄⁺ concentrations (greater than 50 μM) were measured in the north Delta tidal transition zone, in the Sacramento River reaches, just downstream from the EchoWater Facility’s effluent inflow location in 2018 and 2020, before the wastewater treatment plant upgrade (fig. 10; table 1.1). The high variability in NH₄⁺ concentrations in this zone in 2018 and 2020 primarily is a result of hourly changes in the ratio of effluent flow to river flow, which determines effluent dilution (O’Donnell, 2014; Kraus and others, 2017b). As expected, NH₄⁺ concentrations were much lower in the north Delta tidal transition zone in 2021 and 2022 after the BNR upgrade, at 3.3 and 0.3 μM median concentrations, respectively (figs. 9–10; table 1.2).

Farther downstream from the EchoWater Facility, in the Cache Slough complex channel system and western Delta tidal zone, similar patterns in NH₄⁺ concentration were observed; the maximum values decreased after the upgrade (figs. 9–10; tables 1.3–1.4). Suisun Bay had lower NH₄⁺ concentrations in the 2 years prior to the upgrade compared to the 2 years after (figs. 9–10; table 1.5, discussed below). In the central Delta tidal zone and Mokelumne system tidal transition zone, maximum NH₄⁺ concentrations during the first two surveys (pre-BNR upgrade) were greater than 15 μM, whereas the highest measured concentrations were near 3 μM during the latter two surveys (fig. 9; tables 1.6–1.7). One key difference in NH₄⁺ concentration trends between the two zones, however, can be seen in the Mokelumne system tidal transition zone in spring 2020, where the median NH₄⁺ concentration of 7.2 μM was the highest out of the four surveys (fig. 9; table 1.7). This difference is because the DCC was open just before the 2020 spring survey, allowing Sacramento River water that contained effluent-derived NH₄⁺ to flow into this zone, whereas the zone was isolated from these inputs by DCC gate closures in other years (fig. 10; table 6). In spring 2020, elevated NH₄⁺ concentrations that extended into the Mokelumne River indicate that even short periods of opening the DCC gates can alter water quality in the Mokelumne River tidal transition zone.

Concentrations of NH₄⁺ in Suisun Bay, the south Delta tidal transition zone, and the San Joaquin tidal transition zone were less variable through time than the other zones, with no clear trends associated with the EchoWater Facility upgrade (figs. 9–10). Concentrations of NH₄⁺ in these areas are less affected by inputs from the Sacramento River and more affected by local point and non-point sources, including other riverine or wetland inputs, other wastewater treatment plants, or internal biogeochemical cycling. Notably, trends of increasing maximum NH₄⁺ concentrations through time were measured in Suisun Bay and the San Joaquin tidal transition zone (figs. 9–10). In spring 2022, well after the upgrade, median NH₄⁺ concentrations in the San Joaquin tidal transition zone and Suisun Bay (each ~5 μM) were higher than the north Delta tidal transition zone (0.3 µM, fig. 9; tables 1.2, 1.5, 1.9), indicating that there are other sources of NH₄⁺ to the Delta that need to be considered other than the EchoWater Facility, including the Stockton Regional Wastewater Control Facility and Central Contra Costa Wastewater Treatment Plant (fig. 2). In spring 2021 and 2022, in Suisun Bay, NH₄⁺ concentrations were higher than concentrations measured in the upstream western Delta tidal zone in some areas, indicating local inputs of NH₄⁺ to Suisun Bay (figs. 9–10).

The increase in NH₄⁺ concentrations in 2021, in Suisun Bay, was most notable in deep waters (fig. 10). Suisun Bay receives nutrient inputs locally from the Central Contra Costa Sanitary District Wastewater Treatment Plant and Suisun marsh, which likely contributed to higher NH₄⁺ concentrations (fig. 2). However, the increased position of X₂ (table 6) at the time of the 2021 spring survey may have also played a role; higher salinity indicates less dilution of freshwater inputs, and higher salinity may have affected phytoplankton community dynamics in a way that resulted in lower NH₄⁺ uptake by phytoplankton. The patches of Suisun Bay that indicate depleted NH₄⁺ concentrations are spatially associated with higher chlorophyll concentrations (see the “Phytoplankton Abundance and Species Composition” section).

In addition to examining where we observed higher NH₄⁺ concentrations, it is relevant where we observed very low values of NH₄⁺, particularly before the upgrade, because it indicates locations where NH₄⁺ sinks (for example, nitrification or uptake by phytoplankton, plants, and bacteria) are greater than NH₄⁺ sources (for example, inputs, remineralization, and benthic release). These locations appear to include the northern part of the Cache Slough complex channel system and areas off the Mokelumne River, including Hog, Sycamore, and Fourteenmile Sloughs (figs. 2, 10).

Nitrate

Main findings are listed here:

Nitrate concentrations across the Delta revealed a larger range than NH₄⁺; NO₃⁻ concentrations were greater than 300 µM in the San Joaquin tidal transition zone during the spring 2022 survey but were below the detection limit (less than 1 μM) in locations above the EchoWater Facility, in the northern part of the Cache Slough complex, and parts of the Mokelumne River and central Delta tidal transition zone (figs. 9–10; tables 1.1, 1.3, 1.6–1.7, 1.9). Because NO₃⁻ concentrations in the San Joaquin tidal transition zone during the spring 2022 survey were about 3 times higher than the highest value in any other survey, these data were replotted without the San Joaquin tidal transition zone to better view trends within other zones (fig. 11).

As expected, NO₃⁻ concentrations increased in the north Delta tidal transition zone after the EchoWater Facility upgrade because of the implementation of the BNR process, which converts effluent NH₄⁺ to NO₃⁻ via nitrification but does not have complete conversion of NO₃⁻ to N₂ gas via denitrification. Just below the EchoWater Facility, median NO₃⁻ concentrations in the Sacramento River were higher in spring 2021 (17.1 μM) and 2022 (10.4 μM) after the BNR upgrades compared to pre-upgrade concentrations measured in spring 2018 and 2020 (7.1 and 7.6 μM, respectively; fig. 11; table 1.2). Conversely, the highest mean, median, and maximum NO₃⁻ concentrations within the north Delta tidal transition zone were measured in 2021, immediately after the EchoWater Facility upgrade (figs. 9–11; table 1.2); this reflects differences not only in effluent nutrient concentration but also effluent dilution, which is a function of effluent discharge volume and river flow.

Unlike NH₄⁺, where the highest concentrations were measured in the Sacramento River just below Freeport due to pre-upgrade effluent inputs from the EchoWater Facility, the highest concentrations of NO₃⁻ were measured on the San Joaquin River. The high concentrations of NO₃⁻ in the San Joaquin River are presumably due to inputs from the Stockton wastewater treatment plant and agricultural return waters (figs. 2, 9–10; Novick and others, 2015; Dahm and others, 2016; Saleh and Domagalski, 2021). The increase in NO₃⁻ concentrations through time in the San Joaquin tidal transition zone seems to be confined to the San Joaquin River south of Fourteenmile Slough (figs. 2, 10), indicating that the San Joaquin River imports water that has higher NO₃⁻ concentration to the Delta. Furthermore, there was a substantial increase of NO₃⁻ concentrations in the San Joaquin tidal transition zone through time. These increases may be due to drought conditions and lower river flows that became more severe in 2021 and 2022.

Higher NO₃⁻ concentrations also appear in the maximum values measured in the central Delta tidal transition zone during the later surveys. However, median NO₃⁻ concentration values in this zone were higher in the first two surveys than the latter two (20.1 and 20.3 µM in 2018 and 2020, respectively, versus 8.0 and 14.7 µM in 2021 and 2022, respectively; table 1.6). Although most of the central Delta tidal transition zone may be decreasing in NO₃⁻ concentration, localized increases over time appear in some areas due to increases in San Joaquin River inputs.

Decreasing maximum NO₃⁻ concentrations occurred through time in the western Delta tidal zone, and 2022 had the lowest median (about 16 versus about 21–24 µM) and minimum (about 7.5 versus about 14–15 µM) values of all four surveys (figs. 10–11; tables 1.4–1.5). In Suisun Bay, NO₃⁻ concentrations included much lower values in 2018, with a range of 7.2–33.1 µM compared to the next three surveys, which had fewer variable concentrations, with ranges of about 22 to 32 µM (figs. 10–11; table 1.5). Similar to NH₄⁺, these lower Susin Bay NO₃⁻ concentrations measured during the spring of 2018 seem to be in the shoals and are associated with a concomitant localized diatom bloom (see the “Phytoplankton Abundance and Species Composition” section). However, median nitrate values in Suisun Bay were similar in 2018, 2020, 2021, and 2022 (26.0, 30.2, 30.2, and 26.4 µM, respectively).

In the Mokelumne system tidal transition zone, the highest median NO₃⁻ value was observed during the spring 2020 survey (13.6 µM; figs. 10–11; table 1.7), attributed to the opening of the DCC gates immediately before the 2020 survey, which allowed effluent containing Sacramento River water to enter this zone (table 6). Median NO₃⁻ concentrations in the Mokelumne system tidal transition zone were similarly low during the 2018 (2.5 µM), 2021 (0.5 µM), and 2022 (1.6 µM) spring surveys, reflecting low NO₃⁻ contributions from the Mokelumne River.

There is no evident trend in NO₃⁻ concentration in the south Delta tidal transition zone through time; however, like in the San Joaquin tidal transition zone, median and maximum NO₃⁻ concentrations peaked in the spring 2022 survey (figs. 10–11). These higher concentrations are thus attributable to higher concentrations entering this zone from the San Joaquin River (figs. 2, 10).

Overall, changes in NO₃⁻ concentrations, both temporally and spatially, were more complicated than that of NH₄⁺. Because the EchoWater Facility treatment plant upgrade BNR process converts NH₄⁺ to NO₃⁻, effluent NO₃⁻ concentrations increased from close to zero to about 8 mg/L of nitrogen (fig. 7) after the upgrade, and thus, NO₃⁻ concentrations in the north Delta transition zone increased in direct response during the spring months. Effects on NO₃⁻ concentration farther downstream are complicated by biogeochemical nutrient transformations and additional inputs (for example, Central San and Stockton wastewater treatment plant inputs and agricultural drainage waters). This information is described in detail in Senn and others (2020), where the downstream effects of the BNR upgrade were broken down into hydrodynamically determined zones of influence (fig. 12). Briefly, before the upgrade, spring NO₃⁻ concentrations largely came from nitrification of effluent-derived NH₄⁺ in much of the Delta. Although NO₃⁻ concentrations in the effluent may have increased with downstream movement from the EchoWater Facility, NO₃⁻ concentrations are expected to decrease because there is less NH₄⁺ to be nitrified.

Dissolved Inorganic Nitrogen

Main findings are listed here:

Although individual examination of NH₄⁺ and NO₃⁻ is important because of their distinct putative environmental effects, DIN (the sum of NH₄⁺ and NO₃⁻) comprises the pool of nitrogen readily available to support primary production. Higher DIN concentrations could yield more phytoplankton biomass. A ratio of 1 µM DIN to 1 µg/L chlorophyll a is commonly used to estimate the potential phytoplankton biomass that can accrue from the available DIN pool (Gowen and others, 1992; Tett and others, 2003; Edwards and others, 2005). Alternatively, at low DIN concentrations (less than 7.1–9.3 µM), phytoplankton growth may become nitrogen limited (Reynolds, 1999; Chorus and Spijkerman, 2021; Cloern, 2021). In addition to absolute concentrations, the percentage of contributions of NH₄⁺ and NO₃⁻ to the total DIN pool (fig. 13) provide information about which form of nitrogen is the predominant contributor. Some studies indicate that nitrogen form may be an indicator of the potential food quality of phytoplankton grown in the Delta, including the growth of harmful algae (Glibert and others, 2016), whereas other studies indicate that nitrogen form is unlikely to be a key driver of phytoplankton community assemblage in the Delta (Ward and Paerl, 2017; Senn and others, 2020; Cloern, 2021).

Temporal and spatial trends in DIN were largely similar to NO₃⁻ concentration (figs. 9–11) because NO₃⁻ is the primary contributor (greater than 60 percent) to DIN across most of the Delta (fig. 13). Exceptions to these trends include areas where NH₄⁺ concentrations were elevated, such as the north Delta tidal transition zone. In this zone, immediately below the EchoWater Facility, DIN concentrations decreased substantially over time, reflecting the implementation of the EchoWater Facility’s BNR upgrade, which reduced effluent DIN inputs by more than 60 percent (fig. 7). Thus, as NH₄⁺ concentrations decreased and NO₃⁻ increased in the north Delta tidal transition zone after the BNR upgrade (in concentration and percentage of contribution to DIN), the median DIN concentrations in this zone decreased through time from 53 µM in 2018 to 35 µM in 2020, 21 µM in 2021, and 11 µM in 2022. Although median DIN concentrations in the zone did not fall below the potential DIN growth limitation threshold value of 9.3 µM (Reynolds, 1999; Chorus and Spijkerman, 2021), concentrations approached the threshold (fig. 11; table 1.2). These data indicate that nitrogen limitation may occur in this zone at times due to variability in the multiple factors that drive these concentrations. In contrast, DIN concentrations in the Sacramento River “control” zone upstream from the EchoWater Facility were potentially limiting to phytoplankton growth during all four spring surveys (median DIN concentrations were 3, 4, 7, and 1 µM in 2018, 2020, 2021 and 2022, respectively; fig. 11; table 1.1). Assessment of whether or not there have been changes in DIN concentrations and forms in this part of the Sacramento River above the EchoWater Facility over time is beyond the scope of this report.

In the Cache Slough complex channel system and western Delta tidal zone, which are zones that predominantly receive flow from the north Delta tidal transition zone and thus are likely to be affected by the EchoWater Facility upgrade, maximum DIN concentrations decreased through time and DIN was lowest during the spring 2022 survey (figs. 10–11; tables 1.3–1.4), with concentrations in the Cache Slough complex channel system falling well below potentially limiting concentrations (9.3 µM). Because these two zones, especially the Cache Slough complex channel system, encompass areas that experience highly variable water residence times (Downing and others, 2016; Gross and others, 2019), changes in median DIN concentrations over time indicate more complicated temporal and spatial trends than the north Delta tidal transition zone, which was more clearly affected by the change in the EchoWater Facility’s effluent.

Similar to NO₃⁻, maximum DIN concentrations in the south Delta tidal transition zone were higher during the spring 2022 survey (49.5 µM) compared to the spring 2018 survey (29.2 µM), with maximum DIN during the 2020 and 2021 surveys similar and near 35 µM (figs. 10–11; table 1.8). This increase from 2018 to 2022 can be attributed to increasing NO₃⁻ concentrations in the San Joaquin tidal transition zone (figs. 9–10). One noticeable spatial pattern within this zone is that Old River generally had lower DIN concentrations than Middle River across each survey, supporting models that indicate Middle River is more hydrologically connected to the San Joaquin River than Old River (figs. 2, 10).

Maximum DIN concentrations increased through time in the central Delta tidal zone, from about 38 µM to about 107 µM, due to higher concentrations entering this zone from the San Joaquin River (figs. 9–11; table 1.6). Median DIN concentrations in the two spring surveys completed after the upgrade in this zone were much lower (about 9 µM in 2021 and about 15 µM in 2022) than the two done before the upgrade (23 µM in 2018 and 2020; table 1.6).

Conversely, maximum DIN concentrations decreased through time in the Mokelumne system tidal transition zone from about 42 to 14 µM (table 1.7), whereas medians remained low (ranging from 1 to 3 µM; table 1.7), except in the spring 2020 survey, where median DIN concentration was noticeably elevated at 24 µM due to opening of the DCC. When viewing the contour map (fig. 10), the 2020 DIN increase in the Mokelumne system tidal transition zone appears restricted to predominantly the North Fork of the Mokelumne River, with the two surveyed dead-end sloughs (Hog and Sycamore Sloughs; fig. 2) displaying a nutrient drawdown that fueled a cyanobacteria bloom (see the “Phytoplankton Abundance and Species Composition” section).

Like observed in NH₄⁺ and NO₃⁻ concentrations, DIN measurements in Suisun Bay exhibited a unique pattern of drawdown on the shoals, with 2018 values having a far wider range and a lower median compared to the more consistent measurements in the later three surveys (fig. 10). These lower Suisun Bay DIN concentrations in 2018 likely are attributed to uptake by a diatom bloom (see the “Phytoplankton Abundance and Species Composition” section; figs. 10–11). However, it can be noted that in addition to DIN uptake by phytoplankton, aquatic vegetation and bacterial communities living in the water column and the benthos may be substantial sinks for DIN, in the form of NH₄⁺ and NO₃⁻ (Senn and others, 2020). These results highlight that uptake of DIN by phytoplankton blooms can draw nutrient concentrations to potentially growth-limiting conditions.

It is evident by the difference in NH₄⁺, NO₃⁻, and DIN concentrations above and below the EchoWater Facility’s effluent discharge location that in spring, when upstream nutrient concentrations are low, the amount and forms of DIN in the Sacramento River are predominantly a function of nitrogen inputs from wastewater treatment facilities and dilution determined by the river discharge (fig. 10). Additional effects on the distribution of DIN forms and concentrations in the Delta include other inputs, hydrologic conditions, biogeochemical processes, and water-management activities (for example, DCC operation, water exports, and barriers). The effects of opening the DCC just before the spring 2020 survey were discussed earlier and are described in the discussion about the coinciding cyanobacteria bloom in the “Phytoplankton Abundance and Species Composition” section.

Another example of the importance of hydrology is evident in three longer water residence time areas surveyed: (1) Cache Slough complex, (2) Hog Slough, and (3) Sycamore Slough (fig. 2). Each of these locations contained low DIN concentrations in the landward, higher water residence time areas, even though tidal action supplies these systems with DIN via advective and dispersive mixing. Low DIN concentrations measured at the landward reaches of these three areas were observed during all four spring surveys regardless of source water DIN concentrations. Because water residence time is higher in these dead-end areas, there is a greater chance for increased phytoplankton growth, which is frequently associated with nutrient drawdown due to DIN uptake by aquatic vegetation and bacteria and denitrification in anoxic sediments (Senn and others, 2020; Stumpner and others, 2020; Bergamaschi and others, 2024). Potential sources of DIN in these areas, including agricultural return waters, benthic fluxes, and mineralization of detrital material, appear to be minimal or offset by sinks.

Phosphate

Main findings are listed here:

Like nitrogen, phosphorus is a required element for all biota. Specifically, PO₄³⁻ is used in processes like the formation of DNA and cell membranes and the production of cellular energy. Dissolved PO₄³⁻ in aquatic ecosystems is readily available for uptake by aquatic vegetation, bacteria, and phytoplankton. When PO₄³⁻ concentrations are above about 0.1–0.3 µM, it can be assumed that phosphorus is readily available and not limiting to phytoplankton growth (Reynolds, 1999; Chorus and Spijkerman, 2021). Below these concentrations there is potential for PO₄³⁻ availability to limit growth; however, dissolved organic phosphorus and particulate phosphorus can also serve as important pools of phosphorus.

Like nitrogen, wastewater treatment plants are primary sources of PO₄³⁻ in many urbanized aquatic ecosystems (Ward and Paerl, 2017). Agricultural and urban drainage waters are other key sources because PO₄³⁻ is commonly used in fertilizers. Although a change in PO₄³⁻ loading was not an objective of the EchoWater Facility’s upgrade (Senn and others, 2020), the implementation of the BNR treatment altered effluent PO₄³⁻ and total phosphorus concentrations (fig. 8). In water year 2018, before phase 1 of the BNR upgrade, PO₄³⁻ concentrations in effluent were about 65–100 µM (2–3 mg/L of P). In water year 2022, after the upgrade, PO₄³⁻ concentrations in effluent were usually below 30 µM (about 1 mg-P/L). It is not clear if these lower PO₄³⁻ concentrations will be maintained in the future because they are not part of the EchoWater Facility’s National Pollutant Discharge Elimination System permit requirements.

Although the implementation of the BNR upgrade led to a decrease in effluent PO₄³⁻ concentrations during most of 2021 and 2022, according to EchoWater Facility’s effluent data, this decrease did not happen until June 2021 (fig. 8). This decrease is reflected in the PO₄³⁻ concentrations observed in the north Delta tidal transition zones during the spring surveys; median PO₄³⁻ concentrations in this zone immediately below the treatment facility were around 3, 2, and 2 µM in 2018, 2020, and 2021, respectively, but concentrations dropped to 0.6 µM in May 2022 (fig. 14; table 1.2). Lower median (and minimum) PO₄³⁻ concentrations in spring 2022 compared to the other 3 years of study were also observed in the western Delta tidal transition zone and Suisun Bay. Because these zones are predominantly made up of Sacramento River water in spring, these lower concentrations are likely a direct result of lower PO₄³⁻ inputs from the EchoWater Facility.

Although water in the Cache Slough complex channel system also is predominantly composed of Sacramento River source water, PO₄³⁻ concentrations in this zone were much more variable because PO₄³⁻ is released from the benthos over time, resulting in higher PO₄³⁻ concentrations in the northern reaches of the Cache Slough complex channel system where water residence times are long and there are extensive shallow water habitats (Bergamaschi and others, 2024). Although the minimum PO₄³⁻ concentration in the Cache Slough complex, associated with the southernmost part of the zone that receives inflowing Sacramento River water, had a lower PO₄³⁻ concentration in spring 2022 compared to the previous studies, the median and maximum values overlapped with the other years (figs. 14–15). These observations reflect the complex biogeochemical transformations that depend on many factors, like water residence time, temperature, water depth, and biota (Xu and others, 2021).

Although there were differences among each mapping event, there were no notable or consistent patterns in PO₄³⁻ concentration in the central Delta tidal zone, the Mokelumne system tidal transition zone, or the south Delta tidal transition zone over time that indicate these areas were affected by the EchoWater Facility upgrade. These zones include complex habitats that can consume and release PO₄³⁻, have longer water residence times than channeled river habitats, and receive inputs from the San Joaquin River.

In the San Joaquin tidal transition zone, PO₄³⁻ concentrations were much higher in 2021 and 2022 compared to 2018 and 2020 (figs. 14–15). Like nitrogen, this increase is presumably associated with the drought conditions and lower dilution of PO₄³⁻ inputs from urban and agricultural sources.

Like the part of the Sacramento River above the EchoWater Facility included in this study, the Mokelumne system tidal transition zone had some of the lowest median PO₄³⁻ concentrations measured across the Delta during the four surveys, ranging from 0.7 to 1.6 µM (figs. 14–15; table 1.7). The highest median value of 1.6 µM in 2020 can be attributed to the opening of the DCC, which routed more nutrient-rich Sacramento River water into this zone. Although low, these concentrations are still well above PO₄³⁻ concentrations of 0.1–0.3 µM considered to be potentially limiting to phytoplankton growth (Chorus and Spijkerman, 2021).

Ratio of Dissolved Inorganic Nitrogen to Dissolved Inorganic Phosphorus

Main findings are listed here:

Optimum DIN and DIP (PO₄³⁻) concentrations and stoichiometry for maximum phytoplankton growth are debated topics among phytoplankton researchers. Whereas a standard optimum DIN:DIP of 16:1, called the Redfield ratio (Redfield, 1934), has been a longtime standard, the reality is that optimum nutrient compositions vary between species and are affected by environmental conditions (Flynn and others, 2010; Hillebrand and others, 2013; Chorus and Spijkerman, 2021). A general pattern confirmed by a meta-analysis by Hillebrand and others (2013) is that diatoms are associated with a lower DIN:DIP ratio than other species, with chlorophytes having higher DIN:DIP and dinoflagellates in between (Ho and others, 2003; Quigg and others, 2003). Cyanobacteria also are associated with higher DIN:DIP compared to the Redfield ratio (Quigg and others, 2011). Although the Redfield ratio of 16:1 is not universally applicable to each phytoplankton taxa, it is a rough mean of global phytoplankton species composition and cellular stoichiometry correlated with high phytoplankton growth rate when nutrients are not in excess (Klausmeier and others, 2004; Hillebrand and others, 2013); thus, we reference DIN:DIP calculated within each Delta zone concerning this longtime standard (fig. 16). Furthermore, DIN:DIP ratios can provide insight into if DIN or DIP is more likely to limit phytoplankton growth and which species of phytoplankton may have a competitive advantage. For example, DIN:DIP values below 16 indicate potential nitrogen limitation whereas higher values indicate potential phosphorus limitation (Chorus and Spijkerman, 2021). However, if both DIN and DIP concentrations are replete, it is unlikely that nutrient limitation is occurring even if the DIN:DIP ratio is not close to 16.

There were only a few instances when the interquartile ranges of DIN:DIP within a specific zone were above the Redfield ratio (and thus more likely to be phosphorus limited than nitrogen limited), and these conditions occurred in zones with high DIN and DIP concentrations that were not likely to be limiting—the north Delta tidal transition zone in 2018 and 2022, Suisun Bay in 2022, and the San Joaquin tidal transition zone in 2022 (figs. 16–17). Interquartile ranges of DIN:DIP within each zone did not intersect the Redfield ratio, except in the north Delta tidal transition zone during the 2020 survey, Suisun Bay during the 2022 survey, and Mokelumne system tidal transition zone during the 2020 survey. All other interquartile ranges fell below the Redfield ratio (fig. 16). These data indicate that during spring in the Delta, phytoplankton blooms are more likely to be nitrogen limited than phosphorus limited. However, as discussed earlier, neither DIN nor DIP concentrations were low enough in much of the Delta during the four spring surveys to be considered potentially limiting to phytoplankton growth (Chorus and Spijkerman, 2021). Exceptions to this conclusion include the Cache Slough complex where DIN concentrations were well below 9 µM, especially in the northern parts (especially in 2022; fig. 10). Potentially limiting DIN concentrations were also observed in the Mokelumne system tidal transition zone, the zone above the EchoWater Facility, and potentially in the central Delta tidal zone after the BNR upgrade.

Observing which zones and during which surveys were either above or below the Redfield ratio in conjunction with the many factors influencing phytoplankton growth (for example, nutrient concentrations, light availability, temperature, salinity, and water residence time) may shed light to which major phytoplankton groups had the highest growth potential and thus competitive advantage concerning nutrients. Because diatoms are associated with lower DIN:DIP (15:1; Hillebrand and others, 2013), it seems as though most of the Delta may comprise nutrient stoichiometry that is favorable to diatoms’ cellular nutrient stoichiometry (figs. 16–17). As mentioned in previous sections, and detailed more thoroughly later in the text, the drawdown associated with lower DIN:DIP in Suisun Bay during the spring 2018 survey coincides with a large diatom bloom (fig. 17; see the “Phytoplankton Abundance and Species Composition” section).

Harmful algal bloom events, including those producing microcystins, are commonly associated with high DIP concentrations (Beaver and others, 2018); however, high DIN:DIP ratios also have been associated with the production of microcystins, which are rich in nitrogen (Quigg and others, 2011). We did observe a large cyanobacteria bloom in the Mokelumne system tidal transition zone during the spring 2020 survey (see the “Phytoplankton Abundance and Species Composition” section) associated with the opening of the DCC, which resulted in higher DIN and DIP concentrations (figs. 14–15) and higher DIN:DIP (figs. 16–17). The diversion of Sacramento River water into the Mokelumne system tidal transition zone may have provided increased nutrients that supported the growth of cyanobacteria.

In the San Joaquin tidal transition zone, DIN:DIP values were generally below 16 during the first three surveys (median ratios of around 9, 14, and 12 in 2018, 2020, and 2021, respectively), but in 2022, the median was highest at 22.5 (table 1.9). DIN and DIP concentrations were higher in 2022 compared to prior surveys (figs. 9–10, 14–15; table 1.9), thus the increase in the DIN:DIP ratio reflects a greater increase in DIN than DIP (fig. 16). Whereas high DIN:DIP indicates nutrient conditions are particularly favorable to harmful algal blooms; DIN and DIP concentrations in the San Joaquin River were well above nutrient-limiting concentrations.

Dissolved Organic Carbon

Main findings are listed here:

Along with particulate organic carbon, the DOC pool serves as an energy source fueling the bacterial food web (Jassby and Cloern, 2000; Stepanauskas and others, 2005). Although DOC can be beneficial from an aquatic habitat standpoint, it is a drinking-water constituent of concern because a fraction of the DOC pool reacts to form disinfection byproducts during treatment (Kraus and others, 2008). Although treated effluent contains DOC, the treatment process is designed to remove most of the biodegradable organic material before release. This process is done by removing solids and by encouraging as much biodegradation and loss (as CO₂) of DOC during treatment. The EchoWater Facility’s current NPDES permit (California Regional Water Quality Control Board, 2021) requires that the biological oxygen demand (BOD) of its treated effluent must be monitored at a daily frequency and maintained below a weekly average of 15 milligrams per liter (mg/L) and a monthly average of 10 mg/L. This permit also requires the facility to report total organic carbon (TOC) concentrations quarterly and DOC concentrations monthly. Although DOC concentrations entering the Delta from the Sacramento River and other riverine inflows affect downstream conditions, higher within Delta contributions of DOC from biota, decomposition of detrital material, agricultural drains, and the benthos also contribute to DOC. Additionally, biogeochemical processing during transport alters DOC concentration and composition (Kraus and others, 2008; Eckard and others, 2020; Richardson and others, 2020).

As described in the “Methods” section, DOC concentrations were modeled at high spatial resolution using a linear empirical relation between in situ fDOM and laboratory-determined concentrations of DOC on discrete samples for each survey. Based on those data, across all four spring surveys, DOC concentrations in the Sacramento River upstream from the EchoWater Facility ranged between 1.2 and 1.6 mg/L of carbon (fig. 18; table 1.1). In the north Delta tidal transition zone immediately downstream from the facility, median DOC concentrations were slightly higher, ranging from 1.4 to 1.9 mg/L of carbon, which is an increase of 0.5, 0.3. 0.1 and 0.0 mg /L of carbon in 2018, 2020, 2021, and 2022, respectively, compared to the zone upstream from the facility (tables 1.1–1.2). This trend over time indicates that after the upgrade, DOC concentrations in treated effluent have, if anything, decreased. This hypothesis is supported by data provided by the EchoWater Facility that indicates TOC and DOC concentrations in their treated effluent were lower after the upgrade (fig. 8).

As Sacramento River water mixed into downstream tidal transition zones, DOC concentrations increased, with many zones doubling in concentration (fig. 18). This increase is in line with several prior studies and models that documented within-Delta contributions of DOC can be substantial (Kraus and others, 2008; Eckard and others, 2020; Richardson and others, 2020). Visual examination of the contour plots provides further insight into which areas of the Delta contribute DOC and why (fig. 19). For example, the northern part of the Cache Slough complex, characterized by longer water residence time, shallow wetlands, organic sediments, and aquatic vegetation, contains higher DOC concentrations than the southern part.

The Mokelumne system tidal transition zone also indicated a large range in DOC concentrations (fig. 18). In the northern reaches, representing water entering the Delta from the Mokelumne River, DOC concentrations were less than 2.0 milligrams of carbon per liter (mg-C/L). Farther downstream within this zone, higher concentrations were observed in Hog and Sycamore Sloughs. Similar to the northern reaches of the Cache Slough complex channel system, the increase in DOC in the dead-end sloughs likely is associated with longer water residence times, which allow for greater inputs from phytoplankton, aquatic vegetation, and soils. These results indicate that ongoing wetland restoration efforts throughout the Delta, which increase water residence time and support primarily production, increase DOC concentrations across the zone.

Moving seaward, the western Delta tidal zone and Suisun Bay displayed smaller ranges in DOC concentration during each survey than the Cache Slough complex channel system, although median values are comparable (figs. 18–19). Within Suisun Bay, notably higher DOC concentrations in the northwest zone in May 2018 and 2021 likely reflects inputs from Suisun marsh to the north.

The highest DOC concentrations typically were observed in the central and southern Delta (at or above 5 mg-C/L; figs. 18–19), presumably reflecting inputs from subsided island agricultural drainage waters that are rich in DOC and mixing with San Joaquin River water that had higher DOC concentration, especially during the 2021 and 2022 drought years. These zones of the Delta also comprise remnant wetlands and have longer water residence times, fostering DOC production by phytoplankton and aquatic vegetation and release from the benthos due to decomposition of detrital material.

DOC concentrations in the San Joaquin tidal transition zone were higher in 2021 and 2022 (median values of 3.9 mg-C/L) compared to 2018 and 2020 (2.8 and 3.4 mg-C/L, respectively). This change likely is a result of drought conditions.

Turbidity

Main findings are listed here:

Turbidity is a measurement of the cloudiness of water and is related to light scattering by particles in the water column. Higher turbidity measurements mean more light is scattered, which shortens the depth to which light useful for photosynthesis can penetrate the water column (the photic zone). Because turbidity directly affects light availability, it is considered one of the main controls on primary production by phytoplankton in the Delta (Cloern, 1987; Stumpner and others, 2020; Richardson and others, 2023b). Turbidity also is a habitat quality characteristic important to zooplankton and fish, including endangered species like the delta smelt, because it affects visibility and thus predator-prey relationships (Cloern, 1999; Vogel and Beauchamp, 1999; Browman and others, 2000; Gallegos, 2001; Kirk, 2010; Rathjen and others, 2012). In addition to providing information about the light field, turbidity is used as a proxy for suspended sediment concentration, which is of interest in the context of contaminant transport, wetland restoration, and mitigation of sea level rise (Kirwan and Megonigal, 2013; Achete and others, 2017).

Environmental factors that may increase turbidity include suspended particulates entering the water in runoff after rain events, erosion due to storm events or construction projects, high flows resulting in bottom shear stress and turbulent conditions, algal blooms, and wind events in shallow water habitats. Suspended particles contributing to turbidity in water bodies can be comprised of matter like algae, bacteria, organic detritus, and mineralic sediment. Because nutrient inputs from wastewater treatment plants are not considered primary drivers of turbidity, there is no expectation that turbidity values would change as a result of the EchoWater Facility BNR upgrade, except perhaps through changes in phytoplankton abundance.

Based on prior studies, we expect higher turbidity in Suisun Bay due to the hydrodynamic trapping and oscillations of suspended particles, followed by the upstream western Delta tidal zone (Schoellhamer, 2011). Across the four surveys, the highest median turbidity values were observed in Suisun Bay (figs. 20–22). The highest median turbidity measurements in Suisun Bay were during the spring 2018 mapping survey (61.3 FNU; fig. 20; table 1.5). This result may reflect the presence of algal particles associated with elevated chlorophyll, coinciding with a diatom bloom (see the “Phytoplankton Abundance and Species Composition” section). The highest maximum turbidity measurements, however, were during the spring 2022 survey, at 197 FNU, which did not coincide with elevated phytoplankton and thus was associated with particle inputs from channels draining Suisun marsh to the north or wind that stirred up bottom sediments. Aside from the high overall turbidity in spring 2018 and high localized turbidity in spring 2022, turbidity values in Suisun Bay remained relatively consistent, with median values in spring 2020–22 near 40 FNU (figs. 20, 22; table 1.5). To better analyze data in zones with lower turbidity values, we replotted the turbidity data shown on figure 20 such that the y-axis is a maximum of 20 FNU (fig. 21).

Trends in turbidity over time are not readily apparent by visual inspection of the data plotted on figures 20–21; however, a few points can be gleaned by examining the same data plotted in the contour maps (fig. 22). The western Delta tidal zone, particularly in the lower Sacramento River in 2020 and 2021, had higher turbidities than other zones of the Delta besides Suisun Bay (figs. 21–22; table 1.4). Higher turbidity observed in the Mokelumne system tidal transition zone during the spring 2020 survey (figs. 21–22; table 1.7) is concomitant with an algal bloom occurring at that time in Hog Slough (see the “Phytoplankton Abundance and Species Composition” section).

Aside from these higher turbidities observed in Suisun Bay, the western Delta tidal zone, and the Mokelumne system tidal transition zone, turbidities measured across other zones of the Delta during the spring surveys were primarily below 15 FNU (figs. 21–22; tables 1.1–1.9). Because turbidity in the Delta is strongly controlled by source inputs, flow conditions, and wind events, further exploration of turbidity data and potential relation to the EchoWater Facility upgrade would be better informed by spring, summer, and fall surveys and long-term trends gleaned from continuous fixed station datasets (Bergamaschi and others, 2020; O’Donnell and others, 2023, 2024; U.S. Geological Survey, 2023).

Water Temperature

Main findings are listed here:

Water temperatures in the Delta are driven by climate, weather, and water management in complex ways that vary across space and time (Bashevkin and Mahardja, 2022). We expected the highest temperatures measured across the four spring surveys to occur during 2020 because although the other surveys were done in May, the 2020 survey was delayed until June due to the coronavirus disease 2019 restrictions (table 2). Although higher water temperatures in 2020 were observed in many zones of the Delta (figs. 23–24), it is not clear this was directly related to the specific timing of the surveys because water temperatures in the Sacramento River above the EchoWater Facility and in the north Delta tidal transition zone were not notably higher in 2020 compared to 2018, 2021 and 2022, and water temperatures above the EchoWater Facility increased by survey date. These data indicate that in spring, flow effects on water residence time and mixing of different water sources to and within the Delta play a large role in determining water temperatures across the system.

Temperatures measured across the Delta during the spring surveys ranged from a low of 16.0 degrees Celsius (˚C) in the Mokelumne system tidal transition zone in 2018 to a high of 25.6 ˚C in the same zone in 2020 (fig. 23; tables 1.1–1.9). Within all but three zones, median water temperature was lowest in 2018 (ranging from 18 to 21 ˚C across zones) and highest in 2020 (ranging from 21 to 24 ˚C across zones; figs. 23–24; tables 1.1–1.9). The exceptions to this trend include the zone above the EchoWater Facility, the north Delta tidal transition zone, and the Cache Slough complex channel system (fig. 23; tables 1.1–1.9). Median temperatures in most zones were lower in 2022 than in 2021, which was driven by differences in climatic and hydrodynamic factors. Temperatures were lower in Suisun Bay and the western Delta tidal zone due to mixing with colder saline water originating from the ocean and because of shorter water residence times compared to other Delta zones.

Salinity

Main findings are listed here:

Because most of the Delta consists of freshwater habitats, this section focuses on salinity measured in Suisun Bay and the western Delta tidal zone (figs. 25–26). Salinity gradients in the Delta are predominantly determined by the mixing of saline water originating from the ocean, with freshwater originating from upstream river flows. During spring, freshwater flows in these two zones largely are determined by water-year type, reservoir releases, exports, and the operation of flow structures like salinity gates and the DCC (table 6).

Because of the drought conditions observed during the surveys, one might expect salinity to increase with each consecutive year because of lower freshwater flows, particularly as the mean Delta outflow during each survey decreased, respectively (table 6). However, median salinity measurements were highest during the 2021 survey (1 practical salinity unit [PSU] in the western Delta tidal zone and about 10 PSU in Suisun Bay) when Delta outflow was 5,308 ft³/s, corresponding to the highest mean X₂ position (84 km) and the lowest mean export:ouflow ratio value (0.11; table 6). These results are an example of how management actions (for example, water diversions) affect water quality. If export:outflow ratio had been maintained at a higher rate more similar to the other surveys, salinity in the western Delta would have been even higher during the 2021 survey.

In 2022, although mean Delta outflow was even lower than in 2021, at 4,955 ft³/s, the position of X₂ was maintained at a similar position (83 km) even given a higher export:outflow ratio (0.16; fig. 6; table 6). This result may be explained by the placement of the west False River Emergency Drought Barrier and several rain events that occurred before the spring 2022 survey. As a result, median salinities in the western Delta tidal zone and Suisun Bay during the spring 2022 surveys were 0.4 and 9.0 PSU, respectively, compared to 1.1 and 9.5 PSU in 2021.

pH and Dissolved Oxygen

Main findings are listed here:

Among the water-quality parameters measured during the four surveys, those most directly reflective of photosynthetic productivity are pH and DO. During photosynthesis, DO is produced and carbon dioxide is removed, elevating pH. The reverse occurs during respiration and decomposition, where DO and pH decrease. Increases in DO and pH are often key indicators of an active phytoplankton bloom (for example, rates of photosynthesis exceed respiration), although high rates of photosynthesis by submerged or floating aquatic vegetation can also cause these patterns. Nitrification (the conversion of NH₄⁺ to NO₂⁻ and NO₃⁻) also consumes oxygen and decreases pH.

There was a decrease in pH immediately below the EchoWater Facility discharge point on the Sacramento River, particularly in the 2018, 2020, and 2021 spring surveys (figs. 27–28) compared to the river reach immediately upstream. This decrease likely is a result of the rapid nitrification of effluent-derived NH₄⁺. This step change seems to become less pronounced over time because the EchoWater Facility upgrades changed the effluent nutrient makeup and lower upstream pH (figs. 7–8, 27–28). Although these pH changes are measurable, the magnitude of change is relatively small (less than 0.5 pH units), and we are not aware of any evidence that these changes affected biological activity in the Sacramento River. Interestingly, maximum pH values in the north Delta tidal transition zone increased with each survey, indicating a reduction in NH₄⁺ inputs from the EchoWater Facility over time may be decreasing oxygen demand from nitrification. However, there was no clear trend in DO percentage of saturation across the four surveys in these northern Delta zones.

Trends in pH and DO across the rest of the Delta during the four spring surveys were more variable. Elevated pH and DO were regularly coincident and thus reflective of high primary productivity. For example, in the Mokelumne system tidal transition zone, pH and DO were regularly elevated in Hog and Sycamore Sloughs compared to the main stem of the South Mokelumne River (figs. 2, 28). The highest measurement of pH (more than 10) also was related to the highest increase in maximum DO (more than 200-percent saturation), which occurred in the Mokelumne system tidal transition zone in 2020 (figs. 27–28). Interestingly, high maximum pH and DO values neither corresponded to the highest median pH nor DO in the same zone during the same surveys, highlighting how patchy changes in water-quality parameters can be (figs. 27–28).

In contrast to the association between elevated pH and DO and phytoplankton blooms observed in the Mokelumne system tidal transition zone, the high pH and DO values observed in the Cache Slough complex channel system during the spring 2020 survey were not associated with a phytoplankton bloom (figs. 27–29). This observation indicates that photosynthesis by aquatic vegetation may increase pH and DO values in this wetland dominated zone.

Within the San Joaquin tidal transition zone, Fourteenmile Slough (fig. 2) generally had higher pH and DO percentage of saturation measurements than the San Joaquin River (figs. 2, 28). This result indicates that higher rates of photosynthesis occur in Fourteenmile Slough (fig. 2), although nutrient concentrations were higher in the San Joaquin River (figs. 2, 10, 15, 28). Like observed in the Cache Slough complex, because there is no evidence that Fourteenmile Slough had higher chlorophyll concentrations, productivity in this zone also may be attributable to aquatic vegetation.

Above the Echowater Facility, North Delta Tidal Transition Zone, and Western Delta Tidal Zone

Water in the main stem of the Sacramento River flows first through the channelized zone above the EchoWater Facility, through the channelized north Delta tidal zone, and then into the more hydrodynamically complex western Delta tidal zone (fig. 2). Bloom events were not recorded during any of the mapping surveys in these three zones, and chlorophyll concentrations in these zones were consistently well below 15 µg/L (fig. 29).

Cache Slough Complex Channel System

Chlorophyll concentrations throughout the Cache Slough complex channel system were similar and low (less than 15 µg/L) during the 2018, 2020, and 2022 surveys, whereas the 2021 survey captured a phytoplankton bloom (as much as 34 µg/L) in the northern part of the Cache Slough complex channel system (figs. 29–30; table 1.3). The highest maximum concentration for each of the four phytoplankton groups were detected in the Cache Slough complex channel system during that bloom (fig. 32; table 1.3). Green algae contributed to total chlorophyll at a higher percentage than any of the three other groups (median of about 39 percent; fig. 32; table 1.3). The phytoplankton enumeration results for the three sites sampled in this zone correspondingly indicated a chlorophyte of the genus Spirogyra, a large filamentous periphyton species, contained the highest biovolume of any species enumerated (greater than 1.8 million cubic micrometers per milliliter [µm³/mL]; fig. 36). Despite the abundance of green algae by cell biovolume, the highest maximum chlorophyll concentration (about 18 µg/L) was on the diatom channel (Bacillariophyta, most commonly; fig. 32; table 1.3). Phytoplankton enumeration results indicate potential diatom genera (and one ochrophyte) that would likely be picked up on the diatom channel, including Melosira, Cocconeis, and Thalassiosira, among others, with no single genus dominating the density or biovolume data (fig. 36).

Each of the three stations in the Cache Slough complex channel system displays unique patterns in phytoplankton species contribution, indicating that the phytoplankton community in this zone is highly variable. Elevated phytoplankton concentrations have been previously reported for areas in the Cache Slough complex channel system that have longer water residence time and shallow water (Stumpner and others, 2020; Brown and others, 2024). It is noteworthy that the Cache Slough complex channel system contained the highest relative abundances of cryptophytes across surveys, though concentrations were below 5 µg/L, with a maximum percentage contribution of 27 percent to overall fluorescence in 2022 (figs. 34–35; table 1.3).

Suisun Bay

Although median chlorophyll concentrations were similar (around 6–10 µg/L, table 1.5) across all four spring surveys in Suisun Bay, there were localized areas that supported higher chlorophyll concentrations around 10–25 µg/L during the 2018 and 2020 surveys (figs. 29–30; table 1.5). The spring 2018 Suisun Bay bloom was more extensive than the spring 2020 bloom but localized to the eastern shoal of Suisun Bay. The 2018 bloom was dominated by diatoms, with diatoms contributing about 70 percent of the total chlorophyll concentration (fig. 34; tables 1.1, 1.5). The 2018 diatom bloom in this part of Suisun Bay also was associated with a drawdown in NO₃⁻ and DIN and higher pH and DO percentage of saturation (figs. 10, 28). The GRIZ station was the nearest location to the spring 2018 Suisun Bay bloom, where discrete samples were collected for phytoplankton enumeration (fig. 1; table 4). In the spring 2018 sample, the dominant species attributing to both biovolume and cell density was the diatom Aulacoseira granulata (fig. 37; Bergamaschi and others, 2020).

During the May 2018 survey, several stations outside of Suisun Bay were dominated by diatom (Bacillariophyta) biovolume and cell density, and particularly by Aulacoseira, yet they did not display similar bloom conditions where chlorophyll was less than 15 µg/L (figs. 2.1–2.2). Comparing phytoplankton enumeration data at station GRIZ with two sites that have similar high density and relative abundance of diatoms (stations 14MILE and NFM, fig. 1; table 4), a noticeable difference is the presence of the diatoms Achnanthidium, Entomoneis, Cyclotella, Cymbella, and Encyonema at GRIZ (fig. 37; Bergamaschi and others, 2020; Richardson and others, 2023a).

In 2020, a less spatially extensive bloom was localized to the central area of Suisun Bay. This bloom was associated with an increase in diatoms and green algae (figs. 34–35, 2.1–2.2). Like the 2018 Suisun Bay bloom, pH and DO percentage of saturation were elevated at the same location as the bloom (figs. 28, 30). However, instead of an overall DIN drawdown, the 2020 Suisun Bay bloom was associated primarily with a drawdown of NH₄⁺ (fig. 10). This drawdown is because the 2018 bloom was larger, and we surmise the phytoplankton took up all the NH₄⁺ pool and then accessed the NO₃⁻ pool (figs. 32–35). During the spring 2020 survey, discrete samples enumerated for phytoplankton at station GRIZ (fig. 1; table 4) were highest in diatom biovolume, attributed to species of the genera Cyclotella and Gyrosigma. However, in terms of cell density, cyanobacteria of the genus Eucapsis were highest (figs. 32–35, 38). Several kinds of green algae were enumerated in the sample collected at station GRIZ in 2020, including Chlorophyta dominated by Chlorella and Euglenophyta, which were not present during the 2018 bloom; however, they do not appear to make up a large part of the biovolume or density in the 2020 sample (fig. 38).

Central Delta Tidal Zone

During the 2018 and 2020 surveys, total chlorophyll concentrations were below 15 µg/L throughout the central Delta tidal zone with median values of 3.4 and 4.7 µg/L, respectively (figs. 29–30). Among the four phytoplankton groups measured, on average, about 28 percent of the total chlorophyll was attributed to diatoms, 45 percent to cyanobacteria, 23 percent to green algae, and less than 1 percent to cryptophytes (figs. 34–35).

There was a large phytoplankton bloom in the central Delta tidal zone during the May 2021 survey, with chlorophyll concentrations of 20–50 µg/L in much of the zone (figs. 32–33). According to the chlorophyll data, diatoms contributed 75–95 percent of these elevated chlorophyll values (median percent contribution of 91 percent; figs. 34–35). Among phytoplankton enumeration data collected from six stations in the central Delta tidal zone during the 2021 spring survey, Aulacoseira was the dominant diatom by biovolume (fig. 39). It also is worth noting that during this period, the cyanobacteria Eucapsis microscopica was similar or higher in density than Aulacoseira, although this species only contributed a small amount to total biovolume. The May 2021 bloom also was associated with elevated DO and pH (figs. 27–28).

Based on high maximum chlorophyll concentration measurements (46 µg/L), another phytoplankton bloom was evident in the central Delta tidal zone during the spring 2022 survey. However, the median chlorophyll measurement during this survey (4 µg/L) was similar to the first two surveys, indicating that the bloom was spatially confined near the west False River Emergency Drought Barrier (figs. 2, 29). Assessing the chlorophyll concentration data separated by algal groupings (figs. 33, 35), indicated patterns were dissimilar from the 2021 diatom bloom because an increase in percentage of green algae is observed with a decrease in percent diatoms (figs. 33, 35). The concentration of green algae was highest directly at the barrier and into Fishermans Cut (figs. 33, 35). It can be noted that the DCC was closed before and during the spring 2022 mapping survey (table 6), and therefore, nutrient inputs from the Sacramento River did not contribute to this event (low DIN within the effluent by 2022 likely did not spur this bloom; fig. 7).

Mokelumne System Tidal Transition Zone

Total chlorophyll concentration in Hog Slough of the Mokelumne system tidal transition zone during the spring 2020 survey was so high (50–450 µg/L) that those data were replotted separately on figure 40. Visual inspection of the chlorophyll contour maps (fig. 30) indicated Sycamore Slough also had elevated chlorophyll during this survey, with values approaching 30 µg/L.

Chlorophyll fluorescence data by phytoplankton group indicated that the elevated chlorophyll in Hog and Sycamore Sloughs during the 2020 survey was attributable mainly to cyanobacteria, with a smaller contribution from green algae (fig. 40). This bloom event coincided with an increase in DIN concentrations in the Mokelumne system tidal transition zone (figs. 10–11), which resulted from the DCC opening before the survey (table 6). The DIN concentration data reflect a drawdown of DIN in Hog and Sycamore Sloughs, which is likely due to DIN uptake associated with these localized blooms (figs. 10–11, 41).

The high DO (as much as 211-percent saturation) and high pH (as much as 10.2) values measured in Hog Slough during the 2020 survey further support that this bloom was actively photosynthesizing (figs. 27–28; table 1.7). Whether or not the 2020 blooms in the Mokelumne system tidal transition zone were supported by the opening of the DCC and delivery of nutrients to this zone will require further investigation—especially because the concentration and form of DIN supplied to this zone via the Sacramento River have changed since the implementation of the BNR upgrade (fig. 7).

Comparing chlorophyll concentrations in the North and South Forks of the Mokelumne River indicated that the South Fork is a more hospitable environment for bloom formation (figs. 2, 42). There are a few hydrologic reasons for this result, including inputs from the higher residence time, dead-end sloughs in the south fork, a lower tidal flow, and shallower water depths (Thompson and others, 2023). Additionally, the South Fork of the Mokelumne River receives less Sacramento River water (for example, effluent flow) than the North Fork (Thompson and others, 2023).

The phytoplankton enumeration data from stations sampled in the Mokelumne system tidal transition zone also indicated that blooms in Hog and Sycamore Sloughs were dominated by cyanobacteria (figs. 2, 43). Stations SYC and SMS (fig. 1; table 4) indicated high cyanobacteria density and biovolume, with the community composition dominated by Dolichospermum and populations of Aphanizomenon and Eucapsis. Phytoplankton enumeration of the sample collected just downstream at station LPS (fig. 1; table 4) indicated only the minor presence of Dolichospermum species (fig. 43). Phytoplankton enumeration of a sample collected at nearby stations NFM and NMR, which contain similar source water but are not hydrologically connected to Hog or Sycamore Sloughs, did not detect either Dolichospermum or Aphanizomenon genera (fig. 43).

The Mokelumne system tidal transition zone also had elevated chlorophyll concentrations during the spring 2021 and 2022 surveys (as much as about 35 and 32 µg/L, respectively; figs. 29–30; table 1.7). However, those blooms were composed primarily of diatoms, with minimal contributions of cyanobacteria (figs. 32–33).

South Delta Tidal Transition Zone

Most of the south Delta tidal transition zone supported low (less than 5 µg/L) populations of phytoplankton; however, there were localized areas of higher values (figs. 29–30, 32–33). This zone is comprised of diverse hydrologic and biogeochemical habitats (for example, remnant wetlands and dead-end channels), thus, there may be areas where specific phytoplankton species grow better. For example, near Clifton Court Forebay, off Old River (fig. 2), a localized increase in cyanobacteria was evident during the 2020 survey (fig. 30). The sample enumerated for phytoplankton at the ORCC station nearest to Clifton Court Forebay (fig. 1; table 4) displays a diverse mixture of several genera of cyanobacteria, including Microcystis, Aphanizomenon, Eucapsis, Dolichospermum, Planktolyngbya, and Planktothrix (fig. 44). Additional stations in the south Delta tidal transition zone contained diverse phytoplankton species composition during the spring 2020 survey (fig. 44).

San Joaquin Tidal Transition Zone

During the four spring surveys, median chlorophyll concentrations in the San Joaquin tidal transition zone ranged from 3.2 to 6.7 µg/L, with concentrations rarely exceeding 10 µg/L (figs. 29–30, 32–33; table 1.9). During the spring 2020 survey, cryptophytes and cyanobacteria were both slightly elevated compared to the other surveys (fig. 32). Density and biovolume measurements of these two groups display interesting results; at station SJRBC, in the San Joaquin tidal transition zone sampled for phytoplankton enumeration during each spring survey, cryptophytes dominate biovolume and cyanobacteria dominate cell density (figs. 1, 45; table 4). The cyanobacteria Eucapsis had the highest cell-density measurements during the 2020–22 spring surveys, according to the phytoplankton enumeration results (fig. 45). However, Eucapsis is a small species and only made up a small contribution to the total biovolume detected in the 2020–22 spring surveys at station SJRBC (fig. 45).

The one occasion when total chlorophyll was detected above 15 ug/L in the San Joaquin transition zone was during the spring 2021 survey. The elevated chlorophyll was attributed to diatoms (fig. 32). Enumeration results from the nearby SJRB station also indicated higher diatom (Bacillariophyta) biovolume during the spring 2021 survey (fig. 45). There was no clear dominant diatom species indicated, with a reported mixture of many species, including Thalassiosira, Cocconeis, and Melosira, among others (fig. 45).