Agricultural pesticides occurring in surface freshwaters can be transported back to land via various transport routes, such as emerging insects or flooding. However, we lack information about whether flooding events can contribute to this transport in smaller agricultural catchments and the potential cascading effect of these pesticides on the recipient food web. We used UHPLC-MS/MS to measure 98 pesticides and metabolites in five riparian plant species and root-zone soils collected in five streams in Southwest Germany. All sampling locations included two paired sites differing in their flooding frequency. Six fungicides and three herbicides were frequently detected in regularly flooded sites. The regularly flooded sites contained more pesticides and higher concentrations compared with the rarely flooded sites. This pattern was present in both plants and root-zone soil, suggesting flooding as a vector for the aquatic−terrestrial transport in small streams. Prosulfocarb, pendimethalin, cyflufenamid, and flufenacet occurred at higher concentrations in plants than in soil, while the opposite result was found for spiroxamine, metrafenone, and boscalid. Our study provides evidence from the field that flooding events, which may increase due to climate change, can transport pesticides to riparian soils and plants with potential cascading effects on terrestrial food webs.