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Open-File Report 2013–1128

Prepared in cooperation with the U.S. Fish and Wildlife Service

Internal Nutrient Sources and Dissolved Nutrient Distributions in Alviso Pond A3W, California

By Brent R. Topping, James S. Kuwabara, Krista K. Garrett, John Y. Takekawa, Francis Parchaso, Sara Piotter, Iris Clearwater, and Gregory G. Shellenbarger

Thumbnail of and link to report PDF (4.2 MB)Executive Summary

Within the Alviso Salt Pond complex, California, currently undergoing avian-habitat restoration, pore-water profilers (U.S. Patent 8,051,727 B1) were deployed in triplicate at two contrasting sites in Pond A3W (“Inlet”, near the inflow, and “Deep”, near the middle of the pond; figs. 1 and 2; table 1, note that tables in this report are provided online only as a .xlsx workbook at Deployments were conducted in 2010 and 2012 during the summer algal-growth season. Specifically, three deployments, each about 7 weeks apart, were undertaken each summer. This study provides the first measurements of the diffusive flux of nutrients across the interface between the pond bed and water column (that is, benthic nutrient flux). These nutrient fluxes are crucial to pond restoration efforts because they typically represent a major (if not the greatest) source of nutrients to the water column in both ponds and other lentic systems.

For soluble reactive phosphorus (SRP, the most biologically available form in solution), benthic flux was positive both years (that is, out of the sediment into the water column; table 2), with the exception of the August 2010 deployment, which exhibited nearly negligible but negative flux. Overall, the average SRP flux was significantly greater at Deep (23.9 ± 8.6 micromoles per square meter per hour (µmol-m-2-h-1); all errors shown reflect the 95-percent confidence interval) than Inlet (12.6 ± 4.9 µmol-m-2-h-1). There was much greater temporal variability in SRP flux in the pond than reported for the lower estuary (Topping and others, 2001).

For dissolved ammonia, benthic flux was consistently positive on all six sampling trips, and similar to SRP, the fluxes at Deep (258 ± 49 µmol-m-2-h-1) were consistently greater than those at Inlet (28 ± 11 µmol-m-2-h-1). Dissolved ammonia fluxes reported for South San Francisco Bay by Topping and others (2001) fall in between these values. Once again, greater variability for benthic fluxes determined in the pond was observed relative to adjacent South San Francisco Bay. With the near absence of any measurable concentration gradient, dissolved-nitrate fluxes were consistently negligible in the pond.

Silica fluxes are often used to represent sediment diagenetic processes that biogeochemically cycle silica (an important algal macronutrient) between biogenic and inorganic phases (Fanning and Pilson, 1974; Emerson and others, 1984). For South San Francisco Bay, those values are consistently positive from core-incubation experiments. In Pond A3W, dissolved-silica fluxes averaged 49 ± 25 µmol-m-2-h-1 at Inlet and were much higher at Deep (482 ± 370 µmol-m-2-h-1), similar to the spatially variability observed for SRP and dissolved ammonia. An elevated silica flux can stimulate diatom production and subsequent eutrophication effects. Variability in these silica fluxes is consistent with season patterns in pond primary productivity.

On the basis of comparisons of dissolved-oxygen flux measurements by profilers and core incubations, it appears that diffusive flux estimates for the sediment in this pond, as one might expected in such benthically productive environments, result in a significant underestimation of true sediment oxygen demand. Therefore, a core incubation experiment was conducted to better quantify the demand.

To complement these benthic-flux studies, a diurnal study of nutrient advective flux into and out of the pond was measured during neap and spring tides to provide comparative estimates for allochthonous solute transport (Garret, 2012). Using the two different tides as the probable upper and lower boundaries, we can estimate a range of probable values throughout the year. After converting this advective flux into kg/yr, we can compare it directly to benthic flux estimates for the pond extrapolated over the 2.27 square kilometer (km2) pond surface. Benthic flux of nitrogen species, averaged over all sites and dates, was about 80,000 kilograms per year (kg/yr), well above the adjective flux range of -50 to 1,500 kg/yr. By contrast, the average benthic flux of orthophosphate was about 12,000 kg/yr, well below the advective flux range of 21,500 to 30,000 kg/yr.

Initial benthic flux estimates were also made for trace metals, including copper, nickel, iron, and manganese. These analyses indicated that the two sites, Inlet and Deep, have different pore-water profiles, with Inlet exhibiting much higher benthic flux estimates for nickel, iron, and manganese.

These initial benthic-flux values reported for macronutrients are particularly impressive in magnitude when one considers that diffusive flux of dissolved solutes based on pore-water profiles provides a conservative determination that may be enhanced by other biogeochemical processes. These enhancement processes (Boudreau and Jorgensen, 2001) include bioturbation, bioirrigation, wind resuspension, and potential groundwater inflows, some of which are captured in core-incubation experiments (Kuwabara and others, 2009). Hence, the values reported herein represent lower bounds to indicate the potential importance of such internal solute sources. The elevated diffusive fluxes for nutrients in the pond relative to the adjacent estuary indicate that vertical nutrient transport between the pond bed and water column is consistently an important (and at times the most important) source of nutrients that stimulate phytoplankton growth in the water column. One might therefore reasonably hypothesize that this benthic transport of biologically reactive solutes (both nutrients and toxicants) represents the most important step at the base of the food web for trophic transfer.

Potential Management Implications

Benthic flux is largely generated by natural and anthropogenic processes that accumulate surface-reactive solutes (that is, certain organic and inorganic nutrients and toxicants) in bed sediment over annual to decadal time scales. It is likely that long-term improvements in water quality within the pond will eventually lead to decreases in contaminant pore-water gradients. However, such decreases are expected to lag in both time and magnitude relative to any surface-water regulatory improvements. This is because the decades-long accumulation of solutes with the sediments will continue to generate a benthic flux until either the solutes diffuse completely into the water column or new sediment lacking the solutes settles sufficiently to diminish the gradient at the sediment-water interface.

There are engineering steps that could be taken to help mitigate the dissolved-oxygen (DO) depletion. Managers could mechanically aerate waters at the pond outflow during low-DO summer periods so that advective transport through the pond could be maximized without compromising receiving water quality. Similarly, if flows can be managed according to diurnal patterns, it would be useful to maximize flow during the day (that is, high DO periods), while also mechanically aerating the pond water column at the inflow and outflow during the night. Inflow water can also be baffled to create turbulence near the inflow, outflow, or both to increase atmospheric oxygen diffusion (that is, increased surface area and mixing).

First posted June 19, 2013

For additional information:
NRP staff
Water Resources National Research Program
U.S. Geological Survey
345 Middlefield Road, MS-435
Menlo Park, CA 94025
National Research Program

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Suggested citation:

Topping, B.R., Kuwabara, J.S., Garrett, K.K., Takekawa, J.Y., Parchaso, F., Piotter, S., Clearwater, I., and Shellenbarger, G.G., 2013, Internal nutrient sources and nutrient distributions in Alviso Pond A3W, California: U.S. Geological Survey Open-File Report 2013–1128, 17 p. and data tables,


Executive Summary



Results and Discussion

Study Design and Methods


References Cited

Data tables

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