We quantified annual nutrient inputs to the Patuxent River estuary from point and nonpoint sources and from direct atmospheric deposition. We also compared nonpoint source (NPS) discharges from Piedmont and Coastal Plain regions and from agricultural and developed lands. Using continuous automated-sampling, we measured discharges of water, nitrogen, phosphorus, organic carbon (C), and suspended solids from a total of 23 watersheds selected to represent various proportions of developed land and cropland in the Patuxent River basin and the neighboring Rhode River basin. The sampling period spanned two years that differed in annual precipitation by a factor of 1.7. Water discharge from the watershed to the Patuxent River estuary was 3.4 times higher in the wet year than in the dry year. Annual water discharges from the study watersheds increased as the proportion of developed land increased. As the proportion of cropland increased, there were increases in the annual flow-weighted mean concentrations of nitrate (NO3-), total nitrogen (TN), dissolved silicate (Si), total phosphate (TPO43-), total organic phosphorus (TOP), total P (TP), and total suspended solids (TSS) in NPS discharges. The effect of cropland on the concentrations of NO3- and TN was stronger for Piedmont watersheds than for Coastal Plain watersheds. As the proportion of developed land increased, there were increases in annual mean concentrations of NO3-, total ammonium (TNH4+), total organic N (TON), TN, total organic C (TOC), TPO43-, TOP, TP, and TSS and decreases in concentrations of Si. Annual mean concentrations of TON, TOC, forms of P, and TSS were highest in the wet year. Annual mean concentrations of NO3-, TNH4+, TN, and Si did not differ significantly between years. We directly measured NPS discharges from about half of the Patuxent River basin and estimated discharges from the other half of the basin using statistical models that related annual water flow and material concentrations to land cover and physiographic province. We compared NPS discharges to public data on point source (PS) discharges. We estimated direct atmospheric deposition of forms of N, P, and organic C to the Patuxent River estuary based on analysis of bulk deposition near the Rhode River. During the wet year, most of the total terrestrial and atmospheric inputs of forms of N and P came from NPS discharges. During the dry year, 53% of the TNH4+ input was from atmospheric deposition and 58% of the NO3- input was from PS discharges; NPS and PS discharges were about equally important in the total inputs of TN and TPO43-. During the entire 2-yr period, the Coastal Plain portion of the Patuxent basin delivered about 80% of the NPS water discharges to the estuary and delivered similar proportions of the NPS TNH4+, TN, TOP, and TSS. The Coastal Plain delivered greater proportions of the NPS TON, TOC, Si, and TP (89%, 90%, 93%, and 95%, respecfively) than of water, and supplied nearly all of the NPS TPO43- (99%). The Piedmont delivered 33% of the NPS NO3- while delivering only 20% of the NPS water to the estuary. We used statistical models to infer the percentages of NPS discharges supplied by croplands, developed lands, and other lands. Although cropland covers only 10% of the Patuxent River basin, it was the most important source of most materials in NPS discharge, supplying about 84% of the total NPS discharge of NO3-; about three quarters of the TPO43-, TOP, TP, and TSS; and about half of the TNH4+ and TN. Compared to developed land, cropland supplied a significantly higher percentage of the NPS discharges of NO3-, TN, TPO43-, TOP, TP, and TSS, despite the fact developed land covered 12% of the basin.