Dynamics of pesticides and their metabolites in drainage waters during baseflow periods and rainfall-runoff events (RREs) were studied from 2014 to 2016 at three small, tile-drained agricultural catchments in Bohemian-Moravian Highlands, Czech Republic. Drainage systems in this region are typically built in slopes with considerable proportion of drainage runoff originating outside the drained area itself. Continuous monitoring was performed by automated samplers, and the event hydrograph was separated using 18O and 2H isotopes and drainage water temperature. Results showed that drainage systems represent a significant source for pesticides leaching from agricultural land. Leaching of pesticide metabolites was mainly associated with baseflow and shallow interflow. Water from causal precipitation diluted their concentrations. The prerequisites for the leaching of parental compounds were a rainfall-runoff event occurring shortly after spraying, and the presence of event water in the runoff. When such situations happened consequently, pesticides concentrations in drainage water were high and the pesticide load reached several grams in a few hours. Presented results introduce new insights into the processes of pesticides movement in small, tile-drained catchments and emphasizes the need to incorporate drainage hydrology and flow-triggered sampling into monitoring programmes in larger catchments as well as in environment-conservation policy.