Purpose Pesticide contamination of river waters is a global problem, and therefore, authorities regularly monitor the water quality status. Especially, flood events might transport large pesticide loads downstream and impact adjacent areas such as sensible floodplain environments by deposing particle bound pesticides or by contaminating the environments by dissolved substances directly. Unfortunately, only little attempts were made to quantify the pesticide pollution of such environments, as the monitoring of soil and sediment contamination is by far more time consuming and complicated compared to the analysis of water samples. Materials and methods In the study presented, we therefore used a holistic approach starting with the reconstruction of the inundation characteristics of a floodplain located in the upper part of the river Elbe, Germany, by using nearby gauging data, screened databases for pesticide concentrations and calculated pesticide loads, and finally, sampled the floodplain soils along an elevation (inundation) gradient. Results As expected, the reconstructed inundation characteristics showed that the low-lying areas of the backwater inflow of the floodplain were flooded more frequently compared to the areas at higher elevation, whereby even the highest elevations sampled were at least flooded during each decade. Furthermore, pesticide concentrations of the river waters and calculated pesticide loads revealed that 13 pesticides can be found regularly, whereby atrazine, terbuthylazine, metazachlor, metolachlor, isoproturon, and chlorotoluron are the main contaminants. Conclusion Concluding, a spatial pattern in the contamination could be detected. High residues of simazine and ethofumesate were associated with areas of less and more frequent inundations, respectively. The transformation products of atrazine and terbuthylazine (2-hydroxy-atrazine and 2-hydroxy-terbuthylazine) were detected, whereby the quantity could be well explained by the inundation characteristics and pesticide loads of the river water.