AbstractFor the first time, a dedicated release of the hydrology and water use model WaterGAP3, has been developed to spatially explicit calculate hydrological fluxes within river basins draining into the Mediterranean and Black Sea. The main differences between the new regional version of the global WaterGAP3 model and the previously applied global version WaterGAP2 can be found in the spatial resolution, snow modeling, and water use modeling. Comparison with observations shows that WaterGAP3 features a more realistic representation of modeled river runoff and inflow into both seas. WaterGAP3 generates more inflow to both seas than WaterGAP2. In the WaterGAP3 simulation, contributions to the total runoff into the Black Sea from individual discharge regions show in general a good agreement to climatology derived runoff, but lesser importance of Georgian rivers for the basin's water. After the successful model validation WaterGAP3 has been applied to correct estimates of seawater mass derived from the GRACE gravity mission and to account for freshwater inflow into both basins. The performance of the WaterGAP3 regional solution has been evaluated by comparing the seawater mass derived from GRACE corrected for the leakage of continental hydrology, to an independent estimate derived from steric-corrected satellite altimetry with steric correction from regional oceanographic models. The agreement is higher in the Mediterranean Sea than in the Black Sea. Results using WaterGAP3 and WaterGAP2 are not significantly different. However the agreement with the altimetry-derived results is higher using WaterGAP2, due to the smaller annual amplitude of the continental hydrology leakage from WaterGAP3. We conclude that the regional model WaterGAP3 is capable of realistically quantifying water mass variation in the region, further developments have been identified.