Continuing negative rainfall anomalies, coupled with climate change projections of increased drought severity and frequency, drive an urgent need to increase resilience and integration in land and water management strategies in many regions of the world. However, complex interactions between land cover change, ecohydrological partitioning and water availability are difficult to quantify, especially at different temporal and spatial scales. In conjunction with local stakeholders, we developed plausible, alternative land use scenarios (including forest diversification and agroforestry schemes) based on the existing four primary land use types (i.e., conifer and broadleaved forests, arable agriculture, and pasture) in a 66 km2 drought‐sensitive catchment in northern Germany. We used modelling to evaluate spatial and temporal changes in water flux partitioning, storage and ages. The spatially‐distributed, tracer‐aided ecohydrological model, EcH2O‐iso, calibrated using hydrometric, ecohydrological and isotopic data at daily time steps from 2007 to 2019 was used in this assessment. The results showed that replacing conifer forests with uneven‐aged mixed forests with younger broad‐leaved trees had the greatest potential for reducing total evapotranspiration and increasing groundwater recharge. For coniferous forests, a 50% increase in the proportion of broad‐leaved trees was projected to result in an 11% increase in groundwater recharge across the catchment. The mixed‐forest management alternatives also reduced groundwater turnover times, which would support more rapid recovery of soil moisture and groundwater stores following droughts. This study demonstrates that such an ecohydrological modelling approach has the potential to contribute useful science‐based evidence for policy makers allowing quantitative assessment of potential land use effects on water availability and effective communication with stakeholders.