Ubiquitous detection of pharmaceuticals in the aquatic environment around the world raises a great public concern. Aquatic residuals of pharmaceuticals have been assumed to relate to land use patterns and various human activities within a catchment or watershed. This study generated a gradient of human activity in the Jiulong River watershed, southeastern China by urban land use percentage in 20 research subwatersheds. Thirty-three compounds from three-category pharmaceuticals [26 compounds of 5 antibiotic groups, 6 compounds of non-steroidal anti-inflammatory drugs (NSAIDs), and 1 compound of respiratory system drugs (RSDs)] were quantified in stream water before the research subwatershed confluences with two sampling events in dry and wet seasons. In total, 27 out of the 33 pharmaceutical compounds of interest were found in stream waters. Seasonality of instream pharmaceuticals was observed, with less compounds and lower concentrations in the wet season sampling event than in the dry season one. Urban land use in the research subwatershed was identified as the main factor influencing in stream pharmaceutical concentrations and composition regardless of season. Rural land uses contributed a mixture of human and veterinary pharmaceuticals possibly from agricultural application of manure and sewage sludge and aquaculture in the research subwatersheds. Erythromycin in both sampling events showed medium to high risks to aquatic organisms. Results of this study suggest that urban pharmaceutical management, such as a strict prescription regulations and high-efficient removal of pharmaceuticals in wastewater treatment, is critical in reducing aquatic pharmaceutical loads.