Intensive agricultural practices increase agrochemical pollution, particularly nitrogen (N) based fertilizers, which present an environmental risk. This study aims to evaluate long-term (2009–2020) data on soil water regime and nitrate dynamics at an agricultural experimental site on fine-textured soils and to better understand the implications of N management in relation to groundwater pollution. The field site is located in the Biđ field (eastern Croatia), in the proximity of the Sava river. Zero-tension lysimeters were installed at six selected locations. Lysimeters were used to monitor the water regime, i.e., outflows in which nitrate concentration was measured, while additional soil-water samples were collected via 4 and 15-meter-deep monitoring wells. Soil hydraulic parameters were estimated by combining the laboratory measurements, and estimation in RETC software. Water regime and nitrate leaching in lysimeters were simulated using HYDRUS-1D for each year to allow crop rotation and to evaluate their effects individually. The HYDRUS-1D model successfully reproduced lysimeter outflows and nitrate dynamics, which was confirmed with high R2 values (water: 93% above 0.7, and nitrate: 73% above 0.7) indicating the good performance of the model simulating nitrification chain reactions. Principal component analysis (PCA) was performed to identify the relationships among all soil properties and environmental characteristics. The results showed the complex interaction of soil hydraulic properties, precipitation patterns, plant uptake, and N application. All locations have a decreasing trend of nitrate leaching over the investigation period. Most of the lysimeter outflows and elevated nitrate concentrations were connected to the wet period of the year when the soil was saturated, and evapotranspiration was low. The results of this study show that it is important to optimize N fertilizer applications for each particular environmental condition to reduce nitrate loss. The study indicates the importance of long-term field studies, key for agro-hydrological modeling and the improvement of agricultural practices.