As water quality in the Chesapeake Bay has declined over recent decades, formerly healthy submersed plant communities have disappeared from littoral areas of the mesohaline estuary. A dynamic simulation model of shallow regions of bay tributaries (<1 m) was developed to investigate growth responses of submersed vascular plants to eutrophication and habitat degradation. Our objectives were to elucidate mechanisms responsible for the decline and to evaluate conditions required for plant restoration and survival. State variables in the model are plant leaves, roots, phytoplankton, epiphytes, and detrital material. The model calculates biomass pools and biogeochemical rate processes over annual cycles with a time step of 6 h. Simulations were performed to investigate the influence of phytoplankton and epiphytes on the underwater light environment, how the balance of limiting resources (light and nutrients) controls growth and productivity of submersed plants, and conditions necessary for the restoration of submersed vegetation. Model output for submersed plants was calibrated to baseline data from the mid 1970s (r(2) = 0.86); simulations reproduced declines in plant biomass with increasing nutrient enrichment. Model experiments showed that by increasing nutrient inputs 40% above levels observed in the 1960s, submersed plants disappeared within 1-2 yr due to enhanced growth of phytoplankton and epiphytes, which reduced light below required levels. Epiphytes were more important than were phytoplankton in attenuating light. The relationship between nutrient enrichment and plant loss rate was complex, as epiphyte density on leaf surfaces was not linearly related to nutrient levels. Relatively small nutrient increases could have a large effect on submersed plants because epiphyte density on leaves increased exponentially as leaf surface area decreased. Exchanges of organic carbon and nutrients between leaf and root compartments were seasonally variable and were critical for survival of submersed plants. The amount of root-rhizome material available for regrowth could control the outcome of nutrient reduction strategies. Consequently, model predictions of plant restoration success were highly dependent on initial conditions. The model is being used successfully as a research tool to interpret ecological relationships in the ongoing reevaluation of management alternatives for submersed plant restoration.