Pesticides are intensely used in the agricultural sector worldwide including smallholder farming. Poor pesticide use practices in this agronomic setting are well documented and may impair the quality of water resources. However, empirical data on pesticide occurrence in water bodies of tropical smallholder agriculture is scarce. Many available data are focusing on apolar organochlorine compounds which are globally banned. We address this gap by studying the occurrence of a broad range of more modern pesticides in an agricultural watershed in Uganda. During 2.5 months of the rainy season in 2017, three passive sampler systems were deployed at five locations in River Mayanja to collect 14 days of composite samples. Grab samples were taken from drinking water resources. In these samples, 27 compounds out of 265 organic pesticides including 60 transformation products were detected. In the drinking water resources, we detected eight pesticides and two insecticide transformation products in low concentrations between 1 and 50 ng/L. Also, in the small streams and open fetch ponds, detected concentrations were generally low with a few exceptions for the herbicide 2,4-D and the fungicide carbendazim exceeding 1 ug/L. The widespread occurrence of chlorpyrifos posed the largest risk for macroinvertebrates. The extensive detection of this compound and its transformation product 3,4,5-trichloro-2-pyridinol was unexpected and called for a better understanding of the use and fate of this pesticide.