This report summarizes results from boat-based, high-resolution water-quality mapping surveys completed before, during, and after upgrades to the EchoWater Resource Recovery Facility (EchoWater Facility), the regional wastewater facility for the City of Sacramento and surrounding areas, near Elk Grove, California. Surveys were completed in the tidal aquatic environments of the Sacramento–San Joaquin Delta (Delta) in spring (May or June) 2018, 2020, 2021, and 2022. In each survey, a suite of in situ sensors were used to continuously (one measurement per second) measure water-quality conditions, nutrients, phytoplankton abundance, and species composition. In addition to in situ data collection, discrete water samples were collected about every 2 miles while underway for determination of phosphate, ammonium, and nitrate concentration. The boat stopped at about 30 locations to collect discrete samples for a suite of additional analytes, including phytoplankton enumeration. The four surveys represent snapshots in time across different phases of the EchoWater Facility Biological Nutrient Reduction (BNR) upgrade. The May 2018 survey represents conditions before the upgrade. The second survey (June 2020) represents conditions after implementation of the Nitrifying Sidestream Treatment. The third survey (May 2021) was completed immediately after the completion of the BNR upgrade and represents a transitional period, and the final survey (May 2022) represents post-upgrade conditions.

Relevant hydrologic and climatic context such as water-year type, X₂ position (the distance from the Golden Gate Bridge to the point upstream where bottom salinity is 2 parts per thousand; Jassby and others, 1995), water export to import ratio, and management actions like the Delta Cross Channel gate operations are presented for each survey so they may be considered in comparisons among surveys. Differences in water-quality parameters, like turbidity, temperature, salinity, pH, and dissolved oxygen (DO) improve understanding of nutrient cycling and phytoplankton dynamics. Because the Delta is a complex system, we divided the study area into hydrologic zones to better examine general trends and obtain a broadscale view of differences among the 4 study years. Results are presented for each survey and parameter using box plots to compare the different hydrologic zones. We also present each parameter using contour maps by survey to display gradients across the system.

The most evident change to water quality in the Delta across surveys is related to the EchoWater Facility BNR upgrade, which included nitrification and denitrification processes. Through this upgrade, effluent ammonium (NH₄⁺) concentrations were reduced by more than 95 percent (from about 2,000 micromolars [μM] to below the reporting limit of 35 μM), and nitrate (NO₃⁻) concentrations increased from near zero to about 500 μM; therefore, the concentration of dissolved inorganic nitrogen (DIN; the sum of NH₄⁺ and NO₃⁻) in the effluent was reduced by about 75 percent between May 2018 and May 2022. The BNR upgrade resulted in a reduction in NH₄⁺ concentrations in aquatic habitats immediately below the facility, designated as the “north Delta tidal transition zone” (Bergamaschi and others, 2024), from about 30 μM pre-upgrade to near zero during the 2022 spring survey, whereas effluent NO₃⁻ increased from median concentrations of about 7 μM to about 15 μM. Because of the reduced effluent nitrogen loads and variability in Sacramento River nitrogen loads from upstream sources, DIN concentrations in the north Delta tidal transition zone decreased from a median of 53.3 μM in 2018 to 35.3 μM in 2020, 20.7 μM in 2021, and 11.3 μM in 2022 during the spring surveys.

The changes in DIN concentration and form observed in the north Delta tidal transition zone after the EchoWater Facility upgrade extended downstream but were rapidly altered by hydrologic mixing, biogeochemical processes, and other nutrient source inputs. Most of the Delta indicated near-zero concentrations of NH₄⁺ 1 year after the completion of the EchoWater Facility upgrades represented by the 2022 survey. Exceptions to this finding were observed in the San Joaquin River near Stockton and in Suisun Bay, indicating there are NH₄⁺ inputs to these locations from other sources (for example, Stockton Regional Wastewater Control Facility and Central Contra Costs Sanitary District wastewater treatment plants or agricultural and urban runoff).

Although there was an increase in NO₃⁻ concentrations in the north Delta tidal transition zone after the upgrade, increases in NO₃⁻ in other zones were not apparent, presumably because nitrification of effluent derived ammonium was no longer a source of NO₃⁻. Concentrations of DIN in many Delta zones were lower in 2022 compared to 2018 and 2020, with concentrations near or below what is considered potentially nitrogen limiting conditions for phytoplankton growth in the North Delta tidal transition zone and the Cache Slough complex channel system. Unrelated to the EchoWater Facility upgrade, NO₃⁻ and therefore DIN concentrations increased in the San Joaquin River near Stockton and in adjacent water bodies by survey date (likely associated with increasing drought conditions). The Mokelumne River had low DIN concentrations, except in 2018 when the Delta Cross Channel was open, which allowed nutrient-rich Sacramento River water to flow into this section of the river. Data from these surveys also support the hypothesis that nutrient drawdown during phytoplankton blooms may create localized nitrogen limiting conditions.

The BNR upgrade resulted in lower effluent phosphate (PO₄³⁻) concentrations, which lowered PO₄³⁻ concentrations in some zones of the Delta during the four spring surveys; however, PO₄³⁻ concentrations throughout the Delta remained above 0.3 μM, indicating that primary productivity was not limited by phosphorous availability. DIN and PO₄³⁻ decreased after the upgrade in many areas of the Delta, and the DIN to dissolved inorganic phosphorus (DIN:DIP) ratio remained similar to pre-upgrade conditions and was often below the Redfield Ratio of 16, indicating nitrogen is more likely to limit phytoplankton growth than phosphorous. Inputs of dissolved organic carbon (DOC) from the EchoWater Facility are a minor source of this constituent to the Delta, so the upgrade had little to no effect on DOC concentrations across the Delta.

Because phytoplankton abundance and species composition in the Delta are shaped by multiple factors other than nutrients (for example, light availability, temperature, salinity, and predation), it is important to consider these factors (as well as long-term monitoring) in addition to the EchoWater Facility upgrade. Although phytoplankton populations were low across much of the Delta during the spring surveys, several localized phytoplankton blooms (defined here as greater than 15 micrograms per liter [μg/L] of chlorophyll) provide insight into conditions that may favor the growth of beneficial and harmful species.