Multi-year nitrogen (N) and phosphorus (P) budgets were developed for the Patuxent River estuary, a seasonally stratified and moderately eutrophic tributary of Chesapeake Bay. Major inputs (point, diffuse, septic, and direct atmospheric) were measured for 13 years during which, large reductions in P and then lesser reductions in N-loading occurred due to wastewater treatment plant improvements. Internal nutrient losses (denitrification and long-term burial of particulate N and P) were measured in tidal marshes and sub-tidal sediments throughout the estuary as were nutrient storage in the water column, sediments, and biota. Nutrient transport between the oligohaline and mesohaline zones and between the Patuxent and Chesapeake Bay was estimated using a salt and water balance model. Several major nutrient recycling terms were directly and indirectly evaluated and compared to new N and P inputs on seasonal and annual time-scales. Major findings included: (1) average terrestrial and atmospheric inputs of N and P were very close to the sum of internal losses plus export, suggesting that dominant processes are captured in these budgets; (2) both N and P export were a small fraction (13% and 28%, respectively) of inputs, about half of that expected for N based on water residence times, and almost all exported N and P were in organic forms; (3) the tidal marsh-oligohaline estuary, which by area comprised ~27% of the full estuarine system, removed about 46% and 74% of total annual upland N and P inputs, respectively; (4) recycled N and P were much larger sources of inorganic nutrients than new inputs during warm seasons and were similar in magnitude even during cold seasons; (5) there was clear evidence that major estuarine processes responded rapidly to inter-annual nutrient input variations; (6) historical nutrient input data and nutrient budget data from drought periods indicated that diffuse nutrient sources were dominant and that N loads need to be reduced by about 50% to restore water quality conditions to pre-eutrophic levels.