This dissertation is an analysis of organic matter cycling using a biogeochemical modeling system to estimate a comprehensive organic carbon budget in an estuary. New processes were built into the model, including sediment-water column dissolved organic matter (DOM) fluxes, wetland input of DOM, and a more sophisticated representation of DOM reactions in the water column. First, the Sediment Flux Model was updated to include DOM as a diagenesis intermediate in the breakdown of organic matter. Long term time series of sediment-water column nitrogen and oxygen fluxes constrained the updated sediment model. On average, subtidal sediment was a net source of 1.00 mol C m-2 yr-1 and 0.19 mol N m-2 yr-1, substantially larger than previous estimates.

Wetland derived DOM undergoes transformations due to absorbing large quantities of UV-Visible light during estuarine transport. To account for this in the model, the light absorbed by DOM drives mechanistic photochemical degradation reactions in a new module in the organic carbon reaction suite. The reaction equations were parameterized and tested by recreating bench top photochemical degradation experiments using the model. Predicted organic carbon transformation rates ranged from 0.59 to 4.86 μmol C L-1 hr-1 and a test data set was recreated with 3.66% mean percent error.

The enhanced modeling system was implemented in the Rhode River, MD, USA, a well studied tributary of Chesapeake Bay. Coupled observations and 3-D modeling results at the outflow of the Kirkpatrick Marsh creek showed that wind variability was important in driving variations in salinity and was strongly correlated with fluorescent DOM. Finally, the fully coupled organic carbon cycle model was implemented and constrained by water column observations. Numerical experiments with and without the tidal wetland input showed that the marsh contributed 20.5% to the total DOC stock within the tributary and 20.7% to the total flux of DOC from the Rhode River to the Chesapeake Bay. A geographic relationship derived from the Rhode River predicts that tidal wetlands contribute 3.0% to the total DOC inputs in Chesapeake Bay and 13.4% to the total DOC stock.