This study presents the results of the influence of the specific geological landforms occurring in a lowland river floodplain on the recharge and drainage conditions in an agricultural area. Particular attention has been paid to the presence of the buried erosional channels of flood waters, which may constitute the preferential paths for migration of agricultural contaminants. Moreover, the changes of effective infiltration which affect the hydrogeological regime of the tested area were analyzed. Priority was also given to the use of laboratory techniques in order to determine the parameters influencing the contaminant migration in the soil-water environment for the purpose of hydrogeological modeling. Laboratory tests, based on a column experiment, were performed in a Trautwein apparatus with reference to the constant head procedure, using conservative and reactive markers. The parameters of advection, dispersion, and sorption, obtained in the laboratory experiment were then used as the input data for the hydrodynamic model of groundwater flow and contaminant migration in the research area. Based on the created digital model of groundwater flow, the multi-variant analysis of the effect of specific geological features on the conditions of contaminant transport in a valley was performed. The presented tools and methods contributed to a significant increase in the accuracy of recognizing zones susceptible to water pollution and should be adopted in other valley areas exposed to contamination.