Row-crop and poultry production have been implicated as sources of water pollution along the Choptank River, an estuary and tributary of the Chesapeake Bay. This study examined the effects of land use, subwatershed characteristics, and climatic conditions on the water quality parameters of a subwatershed in the Choptank River watershed. The catchments within the subwatershed were defined using advanced remotely-sensed data and current geographic information system processing techniques. Water and sediment samples were collected in May–October 2009 and April–June 2010 under mostly baseflow conditions and analyzed for select bacteria, nitrate-N, ammonium-N, total arsenic, total phosphorus (TP), orthophosphate (ortho-P), and particle-phase phosphorus (PP); n = 96 for all analytes except for arsenic, n = 136, and for bacteria, n = 89 (aqueous) and 62 (sediment). Detections of Enterococci and Escherichia coli concentrations were ubiquitous in this subwatershed and showed no correlation to location or land use, however larger bacterial counts were observed shortly after precipitation. Nitrate-N concentrations were not correlated with agricultural lands, which may reflect the small change in percent agriculture and/or the similarity of agronomic practices and crops produced between catchments. Concentration data suggested that ammonia emission and possible deposition to surface waters occurred and that these processes may be influenced by local agronomic practices and climatic conditions. The negative correlation of PP and arsenic concentrations with percent forest was explained by the stronger signal of the head waters and overland flow of particulate phase analytes versus dissolved phase inputs from groundwater. Service roadways at some poultry production facilities were found to redirect runoff from the facilities to neighboring catchment areas, which affected water quality parameters. Results suggest that in this subwatershed, catchments with poultry production facilities are possible sources for arsenic and PP as compared to catchment areas where these facilities were not present.