Regional Monitoring Program 1997 Annual Report

Chapter 3.

Water Monitoring

1.Introduction

2.1997 Review Implementation

3.Water Monitoring

4.Sediment Monitoring

5.Bivalve Monitoring

6.Pilot and Special Studies

7.Related Monitoring Activities

8.Other Monitoring Activities

*Acronyms

*Glossary

*Appendices

Search document

Suspended-solids concentration (SSC) responds differently to seasonal variations, such as Delta outflow and wind in shallow water areas than in deep-water channels. Although San Francisco Bay includes extensive areas of shallow water, with about onehalf of the surface area of the Bay being less than 2 meters deep (Conomos and Peterson, 1977), deep-water channels along the spine of San Francisco Bay, not shallow waters, are generally sampled by the Regional Monitoring Program (RMP; SFEI, 1997) and the U.S. Geological Survey (USGS; Buchanan and Schoellhamer, 1996; Edmunds et al., 1997; Freeman et al., 1997).

The purpose of this article is to provide an example of how SSC varies in shallow water. Time series of SSC were measured at several sites in Honker Bay. Measurements were made from December 1996 to March 1997 to observe the first wintertime freshwater flood pulse pushing salinity out of Honker Bay and delivering the first flush of sediment from the Central Valley watershed to the Bay. Instruments also were deployed from April to August 1997 to measure the return of salinity to Honker Bay as freshwater flow diminished, and to measure resuspension of sediment by windwaves. Honker Bay was chosen because of its ecological significance to many estuarine plants and animals that depend on shallow waters for shelter and nourishment (Atwater et al., 1979; Cloern et al., 1983).

Total concentrations of seven trace elements measured by the RMP are well correlated with SSC (Schoellhamer, 1997a, 1997b). Thus, the spatial and temporal variability of some trace elements of concern to the RMP is analogous to the SSC variability discussed in this article.

Time-Series Data

The USGS collected timeseries data of water velocity, water depth, wind-waves, salinity, temperature, and SSC at six sites in Honker Bay, a shallow subembayment at the landward end of Suisun Bay (Figure 3.52). The four shallow water sites were designated cmid, barse, cse, and back. The two deep-water sites were designated hs2 near the boundary between Suisun Bay and Honker Bay, and hdol near the southeast end of the Suisun Cutoff channel. A continuous SSC monitoring station has been operated by the USGS near Honker Bay at Mallard Island in the deep (13.5 meter) channel at the landward boundary of Suisun Bay (Figure 3.52) since February 1994.

SSC was determined at 10minute intervals with optical backscatterance (OBS) sensors that measure the amount of suspended material in the water, the output of which was converted to SSC using calibration curves developed from the analysis of water samples. Sensors at each of the sampling locations were serviced every three to five weeks to retrieve data, to collect water samples for sensor calibration, and to clean the sensors, which are susceptible to biological fouling.

Spatial Variability

During the winter deployment, all of the sampling locations showed similar temporal SSC trends (Figure 3.53). During the spring deployment, which is more indicative of typical flow and wind conditions, Honker Bay was not a homogeneous environment. For example, data collected at sites cmid and barse show large SSC spikes that persisted for several weeks in late April and early May, probably due to windwave resuspension of sediment at low tide from a bar at the mouth of Honker Bay. In contrast, SSC at site back began to increase in July, which may be because of sediment moving from the bar northeastward towards the head of the Bay. No windwave signal is present at site cse because it is more protected from wind so there is less wind shear to resuspend bottom sediments. Tidally induced variations in SSC, seen as a thicker black band along the baseline of the SSC data, tend to be more dominant at the sites located near the mouth of Honker Bayhdol, cmid, barse, and hs2 (Figure 3.53). These tidally induced variations in SSC are most dramatic at site hdol, which is heavily influenced by tidal action in the Suisun Cutoff channel. In contrast, the SSC time-series at sites cse and back, which are further from the mouth of Honker Bay, exhibit less influence from tidal variations.

A statistical analysis of the SSC data collected during each deployment is presented in Tables 3.5 and 3.6. The winter deployment had less spatial variability between the sites and less sediment in suspension. The site at cse was not in operation during the first deployment.

The mean SSC at each shallow water site during the spring deployment fell between 110 milligrams per liter (mg/L) at site cse to 120 mg/L at site barse (Table 3.6).

Although the mean SSC throughout Honker Bay is similar at each of the sites, there can be considerable differences among the sites at any given time. The standard deviation of the SSC values at sites cmid, cse, and barse for each OBS meter reading during the spring deployment shows that the spatial variability of the SSC data among the sites is also highly variable in time (Figure 3.54). Sites barse, cse, and cmid were used in this analysis because they had the most complete data sets and included data for late April and early May. The standard deviation is greatest in early spring, peaking at 900 mg/L, which corresponds to Krone's (1979) observation that unconsolidated bottom sediments are easily resuspended due to increased windwave action in early spring. Spatial variability is attributable to nonhomogeneous bathymetry, currents, and wind shear in Honker Bay.

For the purpose of this article, site cmid was selected to be a representative site in Honker Bay because it is located in the center of the shallow water study area and displays similar behavior to site barse. The impacts of spatial variability in shallow water on sampling programs are discussed in greater detail in the following sections of this article.

Flood Pulses

The immediate effect of flood pulses is an abrupt increase in SSC in the deep channel and shallow water areas as sediment from the Central Valley watershed is flushed into San Francisco Bay. Estimates of discharge from the SacramentoSan Joaquin River Delta were obtained from the California Department of Water Resources (1986). The first flood pulse of water year 1997 occurred on January 4, 1997 peaking at approximately 524,000 cubic feet per second (ft³/s), and a second flood occurred several weeks later on January 27, 1997 peaking at approximately 274,000 ft³/s (California Department of Water Resources, 1986). Six days of data (January 1­6) were lost at all of the shallow water sites in Honker Bay due to equipment malfunction; however, the Mallard Island SSC monitoring site was operational during this period (Figure 3.52). Increases in the baseline Mallard Island SSC time-series data generally correlate to increases in Delta outflow (Figure 3.55). However, during the second flood pulse, the SSC values were approximately 25 percent of those during the first flood peak even though the magnitude of the second flood peak was more than 50 percent of the first. The diminished SSC response to the second flood pulse is likely due to a lack of available sediment because the first flush reduces the sediment supply by transporting large quantities of the readily erodible material into the Bay (Goodwin and Denton, 1991). Note that the relationship between Delta outflow and SSC is not linear.

In comparing Mallard Island data to site cmid data, there is a marked difference between these two sites after the influx of sediment from the two 1997 flood pulses (Figure 3.55). Both sites have a baseline SSC of 25­50 mg/L before the first flood pulse. Mallard Island approaches baseline concentrations 1­2 weeks after each flood pulse, whereas site cmid reaches higher concentrations than Mallard Island and does not approach baseline concentrations until nearly one month after the second flood pulse.

SSC was greater in Honker Bay than at Mallard Island during January and February because of differences in suspended sediment supply. The dominant suspended sediment source at Mallard Island is flood-derived sediment that is transported past the site and into the Bay. The suspended sediment source at site cmid, however, is a combination of the initial pulse of sediment arriving with the flood waters and sediment resuspension due to tidal currents. The smaller tidal currents in Honker Bay allow sediment deposition on the Bay floor, which are then susceptible to repeated episodes of resuspension and deposition due to tidal currents in January and February. Later in the year, as sediment consolidation progresses, tidal currents alone are not sufficient to resuspend bottom sediments. This recycling of floodderived sediment accounts for greater SSC in Honker Bay than at Mallard Island in January and February. Reservoir releases of water with relatively low SSC after storms also may contribute to the lower SSC at Mallard Island, compared to that at site cmid. In addition, increasing winds at the end of February caused sediment resuspension significantly greater than that produced by tidal currents alone (Figure 3.55).

SSC time-series data in Honker Bay have broadened peaks and lag behind SSC time-series data at the Mallard Island channel site after each flood pulse, indicating that the residence time of floodderived sediment in Honker Bay is longer than in the neighboring channel. Shallow water provides temporary offchannel storage for sediment on the Bay floor, which is slowly depleted through repeated tidallydriven cycles of resuspension, transport, and deposition. Note that baseline concentrations are reached at site cmid about 4 weeks after the second flood pulse (Figure 3.55), whereas seasonal winddriven resuspension generally affects San Francisco Bay for several months (Schoellhamer, 1996, 1997b). Because SSC is well correlated with several trace elements (Schoellhamer, 1997a, 1997b), the trace elements associated with floodrelated sediment will also tend to have longer residence times in shallow water than in the channel.

Wind-Waves

Sediment resuspension by windwaves in shallow water is an important factor controlling SSC during the spring when the wind velocity increases (Krone, 1979; Schoellhamer, 1996, 1997b). Wind blowing over shallow water generates waves that create a shear stress on the Bay floor.

Wind data were measured by the USGS at a continuously operated meteorological station near Honker Bay (Figure 3.52). During the study, the highest SSC values occurred in late April and early May 1997, which corresponds to a period of strong winds, averaging approximately 7.4 meters per second (m/s), and high associated bottom shear stress. Bed shear stress is approximately proportional to the square of the bottom orbital velocity and increases as the water depth decreases (Dean and Dalrymple, 1984). Linear wave theory and spectral analysis of wave data were used to calculate bottom orbital velocity (Schoellhamer, 1995). Even though the relatively large wind and bed shear stresses continued until the end of the study period, spikes in the SSC data cease in May 1997 (Figure 3.56). An explanation for the observed pattern is that, early in the spring, unconsolidated fine sediments can easily be resuspended, however, as the fine sediments are winnowed from the bed, the remaining sediments become progressively less erodible (Krone, 1979; Nichols and Thompson, 1985).

A brief windy period at the end of February 1997 illustrates the effects of windwaves on SSC (Figure 3.57). When the bed shear stress increases, spikes in the SSC at site cmid appear during low tides, and when bed shear dissipates, the SSC spikes decrease. Note that SSC peaks tend to continue even after the wind shear has dissipated, indicating that sediment will tend to remain in suspension for some time after the wind ceases and will be transported past the sample site during one to three tidal cycles before settling on the Bay floor.

Thus, the timing of sample collection for trace elements associated with SSC is important, particularly if only sparse data can be collected. In Honker Bay, the greatest temporal and spatial SSC variability occurs on windy days at low tide in early spring (Figure 3.54 and 3.57). If only a few samples that are representative of spatial and temporal trends can be collected from shallow areas, sampling at low tide on windy days should be avoided, particularly in the early spring. However, if maximum concentrations of trace elements associated with SSC are sought, trace element concentration peaks will most likely occur on windy days at low tide in early spring.

Conclusions

Suspended-solids concentrations respond differently in shallow water areas than in deeper channels to seasonal forces, such as Delta outflow and wind. During flood pulses, particularly during the first flood pulse of the season, SSC increases in both shallow water areas and deep channels. Shallow bays provide temporary offchannel storage for suspended-solids and their associated trace elements, and therefore have higher concentrations than neighboring channels following flood pulses. Subsequent resuspension of unconsolidated bed sediment in shallow water by tidal currents cause SSC in shallow water to take longer to return to baseline concentrations than in the deeper channel water. In early spring, windwaves resuspend fine bed sediments causing the greatest spatial variability of SSC in shallow water. Later in the summer, after fine sediments have been winnowed from the Bay floor, less erodible sediments are left behind and SSC decreases, even though windgenerated bed shear stress remains high. Therefore, spatial and temporal variations in SSC should be considered when developing sampling programs for trace elements associated with suspended sediment.

Acknowledgments

Instrument deployments in Honker Bay were supported by the USGS INATURES Program. The U.S. Army Corps of Engineers, as part of the Regional Monitoring Program, supported several continuous SSC monitoring sites in Central and South San Francisco Bay during water year 1997 and the preparation of this article. Operation of the Mallard Island SSC monitoring site was supported by the California Regional Water Quality Control BoardSan Francisco Bay Region and the USGS Federal/State Cooperative Program. Operation of the Suisun Bay meteorological station was supported by the Interagency Ecological Program and the USGS Federal/State Cooperative Program. Paul Buchanan, Jon Burau, Jay Cuetara, Robert Sheipline, and Brad Sullivan of the USGS and Jessica Lacy of the Department of Civil Engineering at Stanford University assisted with the instrument deployments in Honker Bay. Kim Taylor of the California Regional Water Quality Control BoardSan Francisco Bay Region, Janet Thompson of the USGS, and Jessica Lacy reviewed earlier drafts of this article.

References

Atwater, B.F., S.G. Conrad, J.N. Dowden, C.W. Hedel, R.L. MacDonald, and W. Savage. 1979. History, landforms and vegetation of the estuary's tidal marshes. In T.J. Conomos (ed.), San Francisco BayThe Urbanized Estuary. Pacific Division of the American Association for the Advancement of Science, San Francisco. pp. 347­385.

Buchanan, P.A. and D.H. Schoellhamer. 1996. Summary of suspended-solids concentration data, San Francisco Bay, California, water year 1995. U.S. Geological Survey OpenFile Report 96591, 40p.

California Department of Water Resources. 1986. DAYFLOW program documentation and DAYFLOW data summary user's guide.

Cloern, J.E., A.E. Alpine, B.E. Cole, R.L.J. Wong, J.F. Arther, and M.D. Ball. 1983. River discharge controls phytoplankton dynamics in northern San Francisco Estuary. Estuarine, Coastal and Shelf Science 16:415­429.

Conomos, T.J. and D.H. Peterson. 1977. Suspendedparticle transport and circulation in San Francisco Bay and overview: Estuarine Processes, Academic Press, NY. v. 2, pp. 82­97.

Dean, R.C. and R.A. Dalrymple. 1984. Water wave mechanics for engineers and scientists. PrenticeHall, Inc., Englewood Cliffs, NJ. 350p.

Edmunds, J.L., B.E. Cole, J.E. Cloern, and R.G. Dufford. 1997. Studies of the San Francisco Bay, California, estuarine ecosystempilot regional monitoring program results, 1995. U.S. Geological Survey OpenFile Report 9715, 380p.

Freeman, L.A., M.D. Webster, and M.F. Friebel. 1997. Water resources data, California, water year 1996: U.S. Geological Survey WaterData Report CA962, v. 2, 356p.

Goodwin, P. and R.A. Denton. 1991. Seasonal influences of the sediment transport characteristics of the Sacramento River, California: Proceedings of the Institute of Civil Engineers, pt. 2, 91:165­172.

Krone, R.B. 1979. Sedimentation in the San Francisco Bay system. In T.J. Conomos (ed.), San Francisco BayThe Urbanized Estuary. Pacific Division of the American Association for the Advancement of Science, San Francisco pp. 347­385.

Nichols, F.H. and J.K. Thompson. 1985. Time scales of change in the San Francisco Bay benthos. Hydrobiologia 192:121­138.

Schoellhamer, D.H. 1995. Sediment resuspension mechanisms in Old Tampa Bay, Florida. Estuarine, Coastal and Shelf Science 40:603­620.

Schoellhamer, D.H. 1996. Factors affecting suspended-solids concentrations in South San Francisco Bay, California. Journal of Geophysical Research 101(C5):12087­12095.

Schoellhamer, D.H. 1997a. Time series of trace element concentrations calculated from time series of suspended-solids concentrations and RMP water samples. In 1995 Annual Report: San Francisco Estuary Regional Monitoring Program for Trace Substances, San Francisco Estuary Institute, Oakland, CA. pp. 53­55.

Schoellhamer, D.H. 1997b. Time series of SSC, salinity, temperature, and total mercury concentration in San Francisco Bay during water year 1996. In 1996 Annual Report: San Francisco Estuary Regional Monitoring Program for Trace Substances. San Francisco Estuary Institute, Oakland, CA. pp. 65­77.

SFEI. 1997. 1996 Annual Report: San Francisco Estuary Regional Monitoring Program for Trace Substances. San Francisco Estuary Institute, Oakland, CA. 299p.