Date of Award

Winter 2002

Document Type


Degree Name

Doctor of Philosophy (PhD)


Ocean & Earth Sciences

Committee Director

Gregory A. Cutter

Committee Member

Eileen Hofmann

Committee Member

Samuel N. Luoma

Committee Member

James G. Sanders


Due to recent concerns about selenium toxicity in the San Francisco Bay and the roles of refinery and San Joaquin River inputs on the selenium cycle, the model ECoS 3 (distributed from Plymouth Marine Laboratory, United Kingdom) was modified to simulate the biogeochemical cycle of selenium in the Northern Reach. The model is designed to simulate salinity, total suspended material, phytoplankton concentrations, dissolved selenium and its speciation (selenite, selenate, and organic selenide), and particulate selenium and its speciation (selenite + selenate, elemental selenium, and organic selenide). Actual data from 1999 were used to calibrate the model, while data from other sampling periods (1986–1988 and 1997–1998) were then compared to model simulations to verify its accuracy. The sensitivity of the model to specific inputs of selenium was also determined. These results indicate that dissolved selenium is largely controlled by riverine and refinery inputs, while particulate selenium is a function of phytoplankton productivity and riverine inputs of sediment. Forecasting simulations included increasing the San Joaquin River discharge to the Delta and varying refinery discharges to the Bay. These simulation results indicate that total particulate selenium concentrations may increase in the entire Bay to 1 μg g−1 if the San Joaquin Flow is increased. This concentration is twice as high as the current estuarine average particulate selenium and at the level where the concentration of selenium in Potomocorbula amurensis becomes problematic for estuarine predators. Furthermore, simulations suggest that doubling the current refinery loads as selenate have little effect on the particle-associated selenium in the estuary. Simulated data from the model can be used in other models to predict selenium concentrations in higher trophic levels. Furthermore the model can be used as a template to study the biogeochemical cycle of other elements in well-mixed estuaries, and in restoration projects, pollution control and other trophic transfer scenarios.


In Copyright. URI: This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).