Soil parameters in agricultural areas play an important role in the migration of nitrogen compounds to groundwater. Nitrogen loss from subsoil depends on soil permeability, organic content, and soil saturation. Our study evaluates the parameters controlling the migration of nitrogen compounds through selected fine and sandy soils that may affect the quality of groundwater in agricultural areas. The results of this study indicate that denitrification processes that substantially affect ammonium (NH₄⁺) and nitrate (NO₃^-) concentrations take place in fine soils. These processes decrease the flow of nitrogen into groundwater and are indicated by the production of a gashouse phase, a decrease in hydraulic conductivity, and a nitrogen compound concentration in the filtrate that is lower than the maximum concentration. Column tests have shown that the dominant transport process for silt loam and sand samples was advection, and the dominant transport process for loam was dispersion. Moreover, the velocities of NH₄⁺ ion transport were lower than the velocities of water flow by approximately seven and five times for loam and sand, respectively. The estimated values of the retardation factor and dynamic sorption capacity for NO₃^- were lower than those for NH₄+ ions. Finally, groundwater located below the silt loam and loam soil layers can effectively be protected against the infiltration of nitrogen compounds from agricultural sources.