Land cover and agricultural management practices can significantly influence soil structure. However, little is known about how fertilizer applications and land cover affect soil hydrology and groundwater recharge over long time periods. The objective of this study was to use stable water isotopes as environmental tracers to provide additional information required for better understanding of water flow and solute transport processes in the unsaturated zone influenced by land cover and type of fertilizer applications. Five lysimeters containing undisturbed soil monoliths from the same agricultural field site were investigated over a period of 5 yr. Liquid cattle slurry and solid animal manure were applied to the maize (Zea mays L.) and winter rye (Secale cereale L.) lysimeters. The grass–clover lysimeter was treated with mineral fertilizer. Quantitative influence of land cover and type of fertilizer application on water flow and solute transport was evaluated for all lysimeters using a modified version of HYDRUS-1D. The highest drainage was observed in the maize lysimeter treated with cattle slurry, and the lowest in the grass lysimeter treated with mineral fertilizer. Pronounced differences in water contents and estimated saturated hydraulic conductivities between the lysimeters were restricted to the upper 25 to 30 cm of the soil. In particular, the lysimeters treated with animal manure had higher porosities, indicating a higher content of organic matter. Main differences in discharge between the lysimeters were observed in spring and during the plant growth periods, indicating the importance of nonuniform, patchy infiltration patterns during snow melt and of root water uptake, respectively. Mean water flow velocities, transit times, and effective water contents were estimated from the stable water isotope data, providing evidence on the impact of land cover and type of fertilizer application. We found smaller mean transit times in the maize lysimeters and for soils with liquid cattle slurry applications. Simulations indicate that numerical modeling can reproduce the general trend of water flow and isotope transport. Despite differences in mean transit times, fitted dispersivities were all in the same range, suggesting similar soil structures in the five lysimeters. However, more data for calibration and more information about heterogeneous infiltration would be required to improve the model accuracy. In general, stable water isotopes clearly contributed an added value, elucidating differences in mean flow parameters between the lysimeters. Thus, they provided evidence of the impacts of land cover and fertilizer applications, which are not obvious from water balance and mean discharge rates alone.