Thesis (Ph. D.)--Stanford University, 2005. / Includes bibliographical references (leaves 273-309).

Population abundances of English sole within the San Francisco Bay from 1973 to 1981 showed a significant positive correlation with Delta outflows, and a significant negative correlation with salinity. Temperature in the bay and ocean upwelling showed no correlation with English sole abundance in the Bay. Because of the positive correlation between the abundance of English sole in the South San Francisco Bay and Delta outflow, this study suggests that any factor resulting in a reduction in outflow may reduce the abundance of English sole in the sample area.

Reliable estimates of river discharge and sediment transport to the ocean from large tidal rivers are vital for water resources management, efficient river and harbor management, navigational purposes, and climate analyses. Due to the difficulties inherent in measuring tidal-river discharge, hydrological and sedimentological records are typically too short to adequately characterize long-term (decadal) trends. Also, uncertainties associated with observation and calibration of hydrological models suggest a need for more accurate methods based on longer records of hydrodynamic parameters (e.g. tides). Tidal theory indicates that tides and river discharge interact through quadratic bed friction, which diminishes and distorts the tidal wave as discharge increases. In this study, using tidal constituents, astronomical forcing and a model of the frictional interaction of flow and tides, I propose a novel Tidal Discharge Estimate (TDE) to predict freshwater discharge with an approximate averaging interval of 18 days for time periods with tidal data but no river flow records. Next, using continuous wavelet analysis of tidal properties, I develop a method of estimating river discharge using tides measured on multiple gages along tidal rivers to improve the time-resolution and accuracy of TDE. The applicability of the Multiple-gauge Discharge Estimate (MTDE) is first demonstrated in the two largest tidal-fluvial systems of the Pacific Northwest, the Columbia River Estuary (CRE) and Fraser River Estuary (FRE). A numerical model of an idealized estuary with similar forcing as the FRE and CRE is next run under different hydrologic and morphologic scenarios to evaluate the effect of convergence, friction, and river flow variations on the applicability of MTDE. The TDE method was applied to the San Francisco Bay, using the continuous hourly tide record available since 1858. Results show that TDE reproduces known San Francisco (SF) Bay delta inflows from 1930-present with a Nash-Sutcliffe coefficient of 0.81 and is a useful method for hindcasting historical flows from 1858 - 1929, a period that predates direct measurement of delta discharge. I also recover and digitize ~80 years of Sacramento River daily water level data between 1849 and 1946, from which river discharge to SF Bay is estimated on a daily basis, after adjusting for changes to the river channel. This discharge combined with Net Delta Outflow Index estimates (1930 - 2011) and flow estimates from tidal data (1858 - 2011) provides a more accurate version of SF Bay historic daily inflows from 1849 - 2011. Next, the history of sediment transport and discharge into SF Bay from 1849-present is reevaluated using the daily discharge estimates. A non-stationary rating curve between river flow and sediment transport is developed, with net sedimentation observed during five bathymetric surveys that were used to constrain the total integrated sediment discharge. Results show that ~1600±320 million-tons of sediment have been delivered to SF Bay between 1850 and 2011. There has been an approximately 25 - 30% reduction of annual flow since the 19th century, along with decreased sediment supply. This has resulted in a ~60% reduction in annual sediment delivery to SF Bay. The annual hydrograph of inflow to SF Bay and the seasonality of sediment flux have changed considerably over time, due to both human alteration and climate change. Significant historic spring-melt peak floods have disappeared in the modern system and now peak flows mostly occur in winter. My flow estimation methods also confirm that the flood of January 1862 had the largest daily sediment load and the second largest daily discharge since 1849.

Thesis. 1975. M.C.P.--Massachusetts Institute of Technology. Dept. of Urban Studies and Planning. / Bibliography: leaves 178-180. / M.C.P.

Thesis (M.S./M.C.R.P.)--California Polytechnic State University, 2009. / Mode of access: Internet. Title from PDF title page; viewed on Jan. 11, 2010. Major professor: Dr. Cornelius Nuworsoo. "Presented to the faculty of California Polytechnic State University, San Luis Obispo." "In partial fulfillment of the requirements for the degrees [of] Master of Science in Engineering/Master of City and Regional Planning (Transportation Planning Specialization)." Includes bibliographical references (p. 194-196).

Calif., Univ., Dep. of Civil and Environment Engineering, Diss.--Stanford, 2003. / Kopie, ersch. im Verl. UMI, Ann Arbor, Mich.

Thesis (Ph.D.); Submitted to the University of California, Berkeley, CA (US); 1 Sep 2003. / Published through the Information Bridge: DOE Scientific and Technical Information. "LBNL--54222" Fine, James. USDOE. Assistant Secretary for Fossil Energy. Office of Natural Gas and Petroleum Technology through the National Petroleum Technology Office (US) 09/01/2003. Report is also available in paper and microfiche from NTIS.

Thesis (M.S.)--University of California, Santa Cruz, 2001. / Typescript. Includes bibliographical references (leaves 69-72).

The primary motivation of this study is to analyze the 1D-2DH hydrodynamic model of the San Francisco Bay and Sacramento-San Joaquin Delta (SFBD) outlined in Nederhoff et al. (2021). I compared model water level data to 70 tidal records from the National Oceanic and Atmospheric Association (NOAA), the United States Geological Survey (USGS), the California Data Exchange Center (CDEC), and from local municipalities throughout the Bay Area to investigate how the model captures water levels and tidal constituent amplitudes. While the Nederhoff et al (2017) model analyzed an extended time period from 1950-2019, I analyzed M2 amplitude and tidal water levels for the water year of 2017 (WY2017) with a larger dataset that extended into the Sacramento-San Joaquin Delta. Because WY2017 was a high river flow year for the Sacramento Delta, the model was able to be evaluated throughout a large range of flow regimes. I used harmonic analysis through the MATLAB package UTide (Codiga et al. 2011) to assess the model’s ability to replicate M2 amplitudes. I assessed the error for these M2 values as well as for tidal water levels. The average RMSE for M2 amplitude is 0.111 m across the entire model domain during WY2017, performing fairly consistent throughout the model. The one exception being the shallow and complex Grizzly Bay, which performed significantly worse, with RMSE values around 0.5 m. The model better replicated water levels in the 2DH grid representation of the San Francisco Bay ( Attempts to improve the model were mostly unsuccessful. I tried to increase the grid resolution at the Carquinez Strait to improve tidal propagation upstream, but altering the grid caused the coupling between the 2DH grid and 1D network to detach. This prevented the propagation of water flow in either direction at the coupling near Collinsville. The software required to fix this coupling was non-standard and unavailable for my usage, so I was unable to resolve the issue. I also attempted to create a new wind forcing file using in-situ data rather than the ERA5 reanalysis. This new wind forcing made negligible difference in water level and M2 model skill. An experiment in removing river flow showed that riverine impacts on elevating extreme water levels only have effects (>0.05 m) east of the Carquinez Strait. Extreme water levels west of this point in the San Pablo, Central, and South Bays are dominated by tides, storm surge, and to a lesser extent local wind. A decrease in tidal amplitude by river flow potentially decreases flood risk in some parts of the Bay during times of high outflow from the Sacramento-San Joaquin Delta. I also investigated maximum equilibrium effects of constant wind in the two prevailing wind directions (southerly and westerly) of the San Francisco Bay. The wind setup effect become more prominent (>0.05 m) at and above a steady 10 m/s in both directions. This study also showed that wind likely exerts a small influence on tidal properties, especially for winds greater than 10 m/s.

Conventional methods for health assessment of wild-caught and stranded seals were used to describe the disease status of harbor seals in California. Clinical chemistry, infectious disease prevalence, immune function, and contaminant data were collected to evaluate harbor seal health with data collected from three groups of seals. Wild-caught seals of all ages were sampled at two locations: San Francisco Bay (a heavily urbanized estuary) and Tomales Bay (a less developed control site). Stranded seals entered rehabilitation from a more extensive portion of the California coast which included the locations where seals were caught. Hematology reference intervals were generated to provide a baseline for health assessment among the seals. Individual variability in blood variables among seals was affected by age, sex, location, and girth. Disease surveillance focused on pathogens known to cause lesions in harbor seals, zoonoses, and those with terrestrial sources. Specific pathogens of interest were E coli, Clostridium perfringens, Vibrio spp, Campylobacter spp, Salmonella, Giardia, Cryptosporidium, avian influenza virus, Brucella, Leptospira spp., Toxoplasma gondii, Sarcocystis neurona, and Neospora caninum, Leptospira spp, and phocine and canine distemper virus. There was evidence of exposure to all pathogens except for phocine distemper virus. Simple measures of immune response were used to evaluate the immune function of harbor seal pups in rehabilitation that had evidence of previous bacterial infection. The swelling response to a subcutaneous injection of phytohemagglutinin (PHA) was positively associated with growth rate, possibly illustrating the energetic trade-offs between growth and immunity. Blubber contaminant concentrations (PCBs, DDTs, PBDEs, CHLDs, and HCHs) in harbor seal pups were grouped by extent of suckling and strand location. The ratio of PCB:DDT was increased in San Francisco Bay and decreased in Monterey Bay compared with other locations along the coast. Pups that weaned in the wild, lost weight and then stranded had the highest contaminant levels, equivalent to the concentrations detected in stranded adult harbor seals. Dispersal and survival were monitored by satellite telemetry in harbor seal pups released from rehabilitation and recently weaned wild-caught pups to assess the effect of condition, health, and contaminant levels on survival probability. Increased contaminant levels and decreased thyroxine (T4) were associated with decreased survival probability. Increased mass, particularly among the rehabilitated pups, was associated with increased survival probability. This study demonstrates that health and survival of harbor seals pups along the central California coast are impacted by human activities such as contaminant disposal, pathogen pollution and boat traffic, although the variability in individual health measures requires carefully designed studies to detect these effects.