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The aim of the paper is to present a methodical approach for developing a hydrodynamic model of groundwater flow and transport of nitrogen compounds in the area covered by the precision farming system. The study area covers the part of the Vistula River floodplain terrace near Warsaw (Poland), in the vicinity of nature reserves: Wyspy Zawadowskie, Wyspy Świderskie and Łęgi Oborskie. The components of the water balance in the analysed area were determined using the HELP (Hydrologic Evaluation of Landfill Performance) model. In reference to the doses of mineral nitrogen used during precise fertilisation, the scenarios of the spread of nitrogen ions in the soil-water environment were detailed. The results were presented graphically in the form of hydroisohypses and isolines of nitrate and ammonium concentrations. The activity of overbank flows and the effect of the geological settings on the course of aquifer layers in the active exchange zone were taken into consideration when describing groundwater flow. This allowed us to indicate potential paths of intense nitrate migration resulting from the evolution of the fluvial environment. Moreover, "hydrogeological windows" have been identified, where contaminants can freely migrate to usable aquifer in the major groundwater basin. Unlabelled Image • Laboratory tests were conducted to determine parameters for hydrogeological modelling. • Multi-stage approaches for assessing the spread of nitrogen compounds are explained. • Remote sensing tools were applied to recognise hydrogeological windows. • Migration paths of nitrogen compounds were predicted using numerical modelling. [ABSTRACT FROM AUTHOR]