David H. Schoellhamer

Projected Evolution of California's San Francisco Bay-Delta-River System in a Century of Climate Change

BACKGROUND Accumulating evidence shows that the planet is warming as a response to human emissions of greenhouse gases. Strategies of adaptation to climate change will require quantitative projections of how altered regional patterns of temperature, precipitation and sea level could cascade to provoke local impacts such as modified water supplies, increasing risks of coastal flooding, and growing challenges to sustainability of native species. METHODOLOGY/PRINCIPAL FINDINGS We linked a series of models to investigate responses of Californias San Francisco Estuary-Watershed (SFEW) system to two contrasting scenarios of climate change. Model outputs for scenarios of fast and moderate warming are presented as 2010-2099 projections of nine indicators of changing climate, hydrology and habitat quality. Trends of these indicators measure rates of: increasing air and water temperatures, salinity and sea level; decreasing precipitation, runoff, snowmelt contribution to runoff, and suspended sediment concentrations; and increasing frequency of extreme environmental conditions such as water temperatures and sea level beyond the ranges of historical observations. CONCLUSIONS/SIGNIFICANCE Most of these environmental indicators change substantially over the 21(st) century, and many would present challenges to natural and managed systems. Adaptations to these changes will require flexible planning to cope with growing risks to humans and the challenges of meeting demands for fresh water and sustaining native biota. Programs of ecosystem rehabilitation and biodiversity conservation in coastal landscapes will be most likely to meet their objectives if they are designed from considerations that include: (1) an integrated perspective that river-estuary systems are influenced by effects of climate change operating on both watersheds and oceans; (2) varying sensitivity among environmental indicators to the uncertainty of future climates; (3) inevitability of biological community changes as responses to cumulative effects of climate change and other drivers of habitat transformations; and (4) anticipation and adaptation to the growing probability of ecosystem regime shifts.

Singular spectrum analysis for time series with missing data

Geophysical time series often contain missing data, which prevents analysis with many signal processing and multivariate tools. A modification of singular spectrum analysis for time series with missing data is developed and successfully tested with synthetic and actual incomplete time series of suspended-sediment concentration from San Francisco Bay. This method also can be used to low pass filter incomplete time series.

Factors affecting suspended‐solids concentrations in South San Francisco Bay, California

Measurements of suspended-solids concentration (SSC) were made at two depths at three sites in South San Francisco Bay (South Bay) to determine the factors that affect SSC. Twenty-eight segments of reliable and continuous SSC time series data longer than 14 days were collected from late 1991 or 1992 through September 1993. Spectral analysis and singular spectrum analysis were used to relate these data segments to time series of several potential forcing factors, including diurnal and semidiurnal tides, the spring-neap tidal cycle, wind shear, freshwater runoff, and longitudinal density differences. SSC is greatest during summer, when a landward wind shear is applied to South Bay by the afternoon sea breeze. About one half the variance of SSC is caused by the spring-neap cycle, and SSC lags the spring-neap cycle by about 2 days. Relatively short duration of slack water limits the duration of deposition of suspended solids and consolidation of newly deposited bed sediment during the tidal cycle, so suspended solids accumulate in the water column as a spring tide is approached and slowly deposit as a neap tide is approached. Perturbations in SSC caused by wind and local runoff from winter storms during the study period were usually much smaller than SSC variations caused by the spring-neap cycle. Variations of SSC at the study sites at tidal timescales are tidally forced, and nonlinear physical processes are significant. Advective transport dominates during spring tides, when water with higher SSC due to wind wave resuspension is advected to the main channel from shallow water, but, during neap tides, advective transport is less significant. The findings of this and other studies indicate that the tidally averaged transport of suspended solids responds to seasonal variations of wind shear in South Bay.

Variability of suspended-sediment concentration at tidal to annual time scales in San Francisco Bay, USA

Singular spectrum analysis for time series with missing data (SSAM) was used to reconstruct components of a 6-yr time series of suspended-sediment concentration (SSC) from San Francisco Bay. Data were collected every 15 min and the time series contained missing values that primarily were due to sensor fouling. SSAM was applied in a sequential manner to calculate reconstructed components with time scales of variability that ranged from tidal to annual. Physical processes that controlled SSC and their contribution to the total variance of SSC were (1) diurnal, semidiurnal, and other higher frequency tidal constituents (24%), (2) semimonthly tidal cycles (21%), (3) monthly tidal cycles (19%), (4) semiannual tidal cycles (12%), and (5) annual pulses of sediment caused by freshwater inflow, deposition, and subsequent wind-wave resuspension (13%). Of the total variance 89% was explained and subtidal variability (65%) was greater than tidal variability (24%). Processes at subtidal time scales accounted for more variance of SSC than processes at tidal time scales because sediment accumulated in the water column and the supply of easily erodible bed sediment increased during periods of increased subtidal energy. This large range of time scales that each contained significant variability of SSC and associated contaminants can confound design of sampling programs and interpretation of resulting data. Published by Elsevier Science Ltd.

Influence of salinity, bottom topography, and tides on locations of estuarine turbidity maxima in northern San Francisco Bay

Time series of salinity and suspended-solids concentration measured at four locations and vertical profiles of salinity and suspended-solids concentration measured during 48 water-quality cruises from January 1993 to September 1997 are analyzed to describe the influence of salinity, bottom topography, and tides on locations of estuarine turbidity maxima in northern San Francisco Bay, California. Estuarine turbidity maxima form when salinity is present but they are not associated with a singular salinity. Bottom topography enhances salinity stratification, gravitational circulation and estuarine turbidity maxima formation seaward of sills. The spring/neap tidal cycle affects locations of estuarine turbidity maxima. Salinity stratification in Carquinez Strait, which is seaward of a sill, is greatest during neap tides, which is the only time when tidally averaged suspended-solids concentration in Carquinez Strait was less than that observed landward at Mallard Island. Spring tides cause the greatest vertical mixing and suspended-solids concentration in Carquinez Strait. Therefore, surface estuarine turbidity maxima always were located in or near the Strait (seaward of Middle Ground) during spring tide cruises, regardless of salinity. During neap tides, surface estuarine turbidity maxima always were observed in the landward half of the study area (landward of Middle Ground) and between 0–2 practical salinity units.

Wetland Accretion Rate Model of Ecosystem Resilience (WARMER) and Its Application to Habitat Sustainability for Endangered Species in the San Francisco Estuary

Salt marsh faunas are constrained by specific habitat requirements for marsh elevation relative to sea level and tidal range. As sea level rises, changes in relative elevation of the marsh plain will have differing impacts on the availability of habitat for marsh obligate species. The Wetland Accretion Rate Model for Ecosystem Resilience (WARMER) is a 1-D model of elevation that incorporates both biological and physical processes of vertical marsh accretion. Here, we use WARMER to evaluate changes in marsh surface elevation and the impact of these elevation changes on marsh habitat for specific species of concern. Model results were compared to elevation-based habitat criteria developed for marsh vegetation, the endangered California clapper rail (Rallus longirostris obsoletus), and the endangered salt marsh harvest mouse (Reithrodontomys raviventris) to determine the response of marsh habitat for each species to predicted >1-m sea-level rise by 2100. Feedback between vertical accretion mechanisms and elevation reduced the effect of initial elevation in the modeled scenarios. Elevation decreased nonlinearly with larger changes in elevation during the latter half of the century when the rate of sea-level rise increased. Model scenarios indicated that changes in elevation will degrade habitat quality within salt marshes in the San Francisco Estuary, and degradation will accelerate in the latter half of the century as the rate of sea-level rise accelerates. A sensitivity analysis of the model results showed that inorganic sediment accumulation and the rate of sea-level rise had the greatest influence over salt marsh sustainability.

Suspended Sediment Fluxes in a Tidal Wetland: Measurement, Controlling Factors, and Error Analysis

Suspended sediment fluxes to and from tidal wetlands are of increasing concern because of habitat restoration efforts, wetland sustainability as sea level rises, and potential contaminant accumulation. We measured water and sediment fluxes through two channels on Browns Island, at the landward end of San Francisco Bay, United States, to determine the factors that control sediment fluxes on and off the island. In situ instrumentation was deployed between October 10 and November 13, 2003. Acoustic Doppler current profilers and the index velocity method were employed to calculate water fluxes. Suspended sediment concentrations (SSC) were determined with optical sensors and cross-sectional water sampling. All procedures were analyzed for their contribution to total error in the flux measurement. The inability to close the water balance and determination of constituent concentration were identified as the main sources of error; total error was 27% for net sediment flux. The water budget for the island was computed, with an unaccounted input of 0.20 m3s−1 (22% of mean inflow), after considering channel flow, change in water storage, evapotranspiration, and precipitation. The net imbalance may be a combination of groundwater seepage, overland flow, and flow through minor channels. Change of island water storage, caused by local variations in water surface elevation, dominated the tidally averaged water flux. These variations were mainly caused by wind and barometric pressure change, which alter regional water levels throughout the Sacramento-San Joaquin River Delta. Peak instantaneous ebb flow was 35% greater than peak flood flow, indicating an ebbdominant system, though dominance varied with the spring-neap cycle. SSC were controlled by wind-wave resuspension adjacent to the island and local tidal currents that mobilized sediment from the channel bed. During neap tides sediment was imported onto the island but during spring tides sediment was exported because the main channel became ebb dominant. Over the 34-d monitoring period 14,000 kg of suspended sediment were imported through the two channels. The water imbalance may affect the sediment balance if the unmeasured water transport pathways are capable of transporting large amounts of sediment. We estimate a maximum of 2,800 kg of sediment may have been exported through unmeasured pathways, giving a minimum ent import of 11,200 kg. Sediment flux measurements provide insight on tidal to fortnightly marsh sedimentation processes, especially in complex systems where sedimentation is spatially and temporally variable.

Mercury concentrations and loads in a large river system tributary to San Francisco Bay, California, USA†

In order to estimate total mercury (HgT) loads entering San Francisco Bay, U.S.A., via the Sacramento-San Joaquin River system, unfiltered water samples were collected between January 2002 and January 2006 during high flow events and analyzed for HgT. Unfiltered HgT concentrations ranged from 3.2 to 75 ng/L and showed a strong correlation (r2 = 0.8, p < 0.001, n=78) to suspended sediment concentrations (SSC). During infrequent large floods, HgT concentrations relative to SSC were approximately twice as high as observed during smaller floods. This difference indicates the transport of more Hg-contaminated particles during high discharge events. Daily HgT loads in the Sacramento-San Joaquin River at Mallard Island ranged from below the limit of detection to 35 kg. Annual HgT loads varied from 61 +/- 22 kg (n=5) in water year (WY) 2002 to 470 +/- 170 kg (n=25) in WY 2006. The data collected will assist in understanding the long-term recovery of San Francisco Bay from Hg contamination and in implementing the Hg total maximum daily load, the long-term cleanup plan for Hg in the Bay.

Implications for Future Survival of Delta Smelt from Four Climate Change Scenarios for the Sacramento–San Joaquin Delta, California

Changes in the position of the low salinity zone, a habitat suitability index, turbidity, and water temperature modeled from four 100-year scenarios of climate change were evaluated for possible effects on delta smelt Hypomesus transpacificus, which is endemic to the Sacramento–San Joaquin Delta. The persistence of delta smelt in much of its current habitat into the next century appears uncertain. By mid-century, the position of the low salinity zone in the fall and the habitat suitability index converged on values only observed during the worst droughts of the baseline period (1969–2000). Projected higher water temperatures would render waters historically inhabited by delta smelt near the confluence of the Sacramento and San Joaquin rivers largely uninhabitable. However, the scenarios of climate change are based on assumptions that require caution in the interpretation of the results. Projections like these provide managers with a useful tool for anticipating long-term challenges to managing fish populations and possibly adapting water management to ameliorate those challenges.

Constancy of the relation between floc size and density in San Francisco Bay

The size and density of fine-sediment aggregates, or flocs, govern their transport and depositional properties. While the mass and volume concentrations of flocs can be measured directly or by optical methods, they must be determined simultaneously to gain an accurate density measurement. Results are presented from a tidal cycle study in San Francisco Bay, where mass concentration was determined directly, and volume concentration was measured in 32 logarithmically spaced size bins by laser-diffraction methods. The relation between floc size and density is investigated assuming a constant primary particle size and fractal floc dimension. This relation is validated with measurements from several sites throughout San Francisco Bay. The constancy of this relation implies a uniform primary particle size throughout the Bay, as well as uniform aggregation/disaggregation mechanisms (which modify fractal dimension). The exception to the relation is identified during near-bed measurements, when advected flocs mix with recently resuspended flocs from the bed, which typically have a higher fractal dimension than suspended flocs. The constant relation for suspended flocs simplifies monitoring and numerical modeling of suspended sediment in San Francisco Bay.