Vegetation plays a key role in riparian area functioning by controlling water and nitrate (N‐NO3‐) transfers to streams. We investigated how spatial heterogeneity modifies the influence of vegetation transpiration on soil water and N‐NO3‐ balances in the vadose soil of a Mediterranean riparian forest. Based on field data, we simulated water flow and N‐NO3‐ transport in three riparian zones (i.e. near‐stream, intermediate, and hillslope) using HYDRUS‐1D model. We investigated spatio‐temporal patterns across the riparian area over a 3‐year period and future years using an IPCC/CMIP5 climate projection for the Mediterranean region. Potential evapotranspiration was partitioned between evaporation and transpiration to estimate transpiration rates at the area. Denitrification in the forest was negligible, thus N‐NO3‐ removal was only considered through plant uptake. For the three riparian zones, the model successfully predicted field soil moisture (θ). The near‐stream zone exchanged larger volumes of water and supported higher θ and transpiration rates (666±75 mm) than the other two riparian zones. Total water fluxes, θ, and transpiration rates decreased near the intermediate (536±46 mm transpired) and hillslope zones (406±26 mm transpired), suggesting that water availability was restricted due to deeper groundwater. Transpiration strongly decreased θ and soil N‐NO3‐ in the hillslope and intermediate zones. Our climate projections highlight the importance of groundwater availability and indicate that soil N‐NO3‐ would be expected to increase due to changes in plant‐root uptake. Lower water availability in the hillslope zone may reduce the effectiveness of N‐NO3‐ removal in the riparian area, increasing the risk of excess N‐NO3‐ leaching into the stream.