Nitrate leaching through soil layers to groundwater may cause significant degradation of natural resources. The aims of this study were: (i) to estimate soil hydraulic properties (SHPs) of the similar soil type with same management on various locations; (ii) to determine annual water dynamics; and (iii) to estimate the impact of subsoil horizon properties on nitrate leaching. The final goal was to compare the influence of different SHPs and layering on water dynamics and nitrate leaching. The study was conducted in central Croatia (Zagreb), at four locations on Calcaric Phaeozem, Calcaric Regosol, and Calcaric Fluvic Phaeozem soil types. Soil hydraulic parameters were estimated using the HYPROP system and HYPROP-FIT software. Water dynamics and nitrate leaching were evaluated using HYDRUS 2D/3D during a period of 365 days. The amount of water in the soil under saturated conditions varied from 0.422 to 0.535 cm3 cm−3 while the hydraulic conductivity varied from 3 cm day−1 to 990.9 cm day−1. Even though all locations have the same land use and climatic conditions with similar physical properties, hydraulic parameters varied substantially. The amount and velocity of transported nitrate (HYDRUS 2D/3D) were affected by reduced hydraulic conductivity of the subsoil as nitrates are primarily transported via advective flux. Despite the large differences in SHPs of the topsoil layers, the deeper soil layers, having similar SHPs, imposed a buffering effect preventing faster nitrate downward transport. This contributed to a very similar distribution of nitrates through the soil profile at the end of simulation period. This case study indicated the importance of carefully selecting relevant parameters in multilayered soil systems when evaluating groundwater pollution risk.