A comprehensive assessment of pesticide transport in surface waters is challenging due to discharge characteristics and the occurrence of transformation products (TPs). Detailed long-term sampling of pesticide concentrations, including rainfall and pesticide application events, is still lacking to better predict pesticide transport pathways and toxicity within agricultural catchments. In the present study, pesticide and TP transport dynamics were evaluated over a three-year monitoring period, which included 12 stormwater events and 7 dry events. An extensive target screening for 328 pesticides was conducted, while simultaneously performing suspect and nontarget analysis (SNTA) using liquid chromatography high-resolution mass spectrometry. Twenty-one pesticides and two TPs associated with the main crop, rice, were identified as the major pollutants. The risk assessment results, based on the stepwise toxicity data collection, suggested that insecticides, primarily neonicotinoids, exhibited severe ecological risk. Additionally, SNTA revealed the presence of 8 parent compounds and 46 TPs. TPs occurred following parent peak periods, indicating that integrated pesticide monitoring is a practical approach to risk assessment. A precautionary approach using SNTA of parent pesticides and TP identification suggests that the potential aquatic effects of pesticide TPs may be underestimated by a conventional pesticide monitoring strategy.