Net biogeochemical production and transport rates for several variables were computed for the Patuxent River estuary from 1985 to 2003 using a box model. Monthly rate estimates were analyzed for temporal patterns and variability in response to climatic factors and nutrient management. The middle estuary was the most productive estuarine region and was characterized by strong pelagic-benthic coupling. Phytoplankton biomass in this region peaked in spring as fueled by seaward nutrient inputs. Nutrients regenerated from decomposition of this spring bloom were required to support summer productivity.

Improvements of sewage treatment in the watershed resulted in declining point source nutrient loads to the estuary, but water quality did not improve in the mesohaline estuary. Poor water quality in the middle estuary was maintained by persistent non-point nutrient loads, while degrading water quality in the lower estuary correlated with increasing DIN inputs from Chesapeake Bay, high river flow, and declining herbivorous grazing.