The Moulouya basin in Morocco is one of many river basins around the world that are regulated with physical flow control, a range of regulations and storage structures. The water budget of the basin is unbalanced; the available water resources are insufficient for agricultural productivity, nature conservation and ecosystem services. This study evaluates spatial and temporal distributions of actual evapotranspiration, groundwater recharge and surface runoff for the period 2000–2020 using the WetSpass-M model in the Moulouya basin, Morocco. The WetSpass-M model’s input data are created in grid maps with the ArcGIS tool. They include monthly meteorological parameters (e.g., temperature, wind speed, rainfall,), soil map, land cover, topography, slope and groundwater depth. A good correlation has been observed between the simulated groundwater recharge and base flow, with the value of R2 = 0.98. The long-term spatial and temporal average annual precipitation of 298 mm is distributed as 45 mm (15.1%) groundwater recharge and 44 mm (14.8%) surface runoff, while 209 mm (70.1%) is lost through evapotranspiration. The simulated results showed that the average groundwater recharge of 15.1 mm (30%) falls during the summer and spring seasons, while the remaining 29.5 mm (70%) occurs during the winter and autumn seasons. Annually, 2430 million m3 of water recharges to the groundwater system from the rainfall for the entire basin. The study’s findings would help local stakeholders and policymakers in developing sustainable and effective management of available surface water and groundwater resources in the Moulouya basin.