The research of the environmental fate of pesticides has demonstrated that applied compounds are altered in their molecular structure over time and are distributed within the environment. To assess the risk for contamination by transformation products (TP) of the herbicides flufenacet and metazachlor, the following four water body types were sampled in a small-scale catchment of 50 km 2 in 2015/2016: tile drainage water, stream water, shallow groundwater, and drinking water of private wells. The TP were omnipresent in every type of water body, more frequently and in concentrations up to 10 times higher than their parent compounds. Especially metazachlor sulfonic acid, metazachlor oxalic acid, and flufenacet oxalic acid were detected in almost every drainage and stream sample. The transformation process leads to more mobile and more persistent molecules resulting in higher detection frequencies and concentrations, which can even occur a year or more after the application of the parent compound. The vulnerability of shallow groundwater and private drinking water wells to leaching compounds is proved by numerous positives of metazachlor-TP with maximum concentrations of 0.7 μg L −1 (drinking water) and 20 μg L −1 (shallow groundwater) of metazachlor sulfonic acid. Rainfall events during the application period cause high discharge of the parent compound and lower release of TP. Later rainfall events lead to high displacement of TP. For an integrated risk assessment of water bodies, the environmental behavior of pesticide-TP has to be included into regular state-of-the-art water quality monitoring.