Recently, new numerical methods have been applied to weather data for the estimation of water budget, especially when the lack of measured data is considerable. Geostatistics is one of the most powerful approaches when it comes to studying spatially relevant natural phenomena, as it considers the spatial correlation among measurements over a specific study area and provides the associate uncertainty. In this study, we tested the feasibility of using a geostatistical method to provide a reliable estimation of the water budget of the Foro river basin (Central Italy) by comparing the obtained results with those of a traditional yet robust method. The results obtained with the geostatistical approach proved to be in line with the ones from the traditional method. Additionally, it was possible to quantify the uncertainty associated with the discharge values, making the estimates more reliable than the ones obtained with the traditional approach. However, the yearly distribution of river discharge obtained using both methods appeared to be dissimilar to the measured ones. The surface water uses, as well as the regulatory effect of the carbonate and alluvial aquifer regime, may affect the river discharge variability over the year and then can account for similar discrepancies between the inflow and outflow water volumes.