The vadose zone plays a significant role in the hydrological cycle - regulating the transfer of water from the surface to the underground, providing protection, transport, and attenuation of potential groundwater contaminants, hence being an important factor in modeling and understanding hydrological and geochemical processes. The research area in the valleys of the Mura and Drava rivers represents an important water resource for two counties in northwestern Croatia (Varaždin and Međimurje). These are aquifers with intergranular porosity, where agricultural activities and undeveloped sewerage networks have caused nitrogen contamination of groundwater. The main research goal of the project is to clarify the role of the vadose zone in aquifer recharge and the behavior of nitrogen compounds in aquifers with intergranular porosity. Achieving the main goal will be enabled through the following specific objectives: i) determining the rate of effective infiltration of precipitation, recharge from surface water, and vertical/horizontal hydraulic conductivity; ii) monitoring the behavior of nitrogen compounds depending on the degree of saturation and identifying dominant transport processes in the vadose zone; iii) defining geochemical processes of nitrogen compound transformation in the vadose zone; iv) developing a numerical model of water flow and nitrate transport through the vadose zone. These objectives will significantly contribute to understanding groundwater contamination by nitrogen compounds and identifying appropriate measures for protection and sustainable management of groundwater.