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The Mediterranean region is one of the climate hotspots where the climate change impacts are both pronounced and documented. The HyMeX (Hydrometeorological Mediterranean eXperiment) aims to improve our understanding of the water cycle from the meteorological to climate scales. However, monitoring the water cycle with Earth observations (EO) is still a challenge: EO products are multiple, and their utility is degraded by large uncertainties and incoherences among the products. Over the Mediterranean region, these difficulties are exacerbated by the coastal/mountainous regions and the small size of the hydrological basins. Therefore, merging/integration techniques have been developed to reduce these issues. We introduce here an improved methodology that closes not only the terrestrial but also the atmospheric and ocean budgets. The new scheme allows us to impose a spatial and temporal multiscale budget closure constraint. A new approach is also proposed to downscale the results from the basin to pixel scales (at the resolution of 0.25 degrees). The provided Mediterranean WC budget is, for the first time, based mostly on observations such as the GRACE water storage or the netflow at the Gibraltar Strait. The integrated dataset is in better agreement with in situ measurements, and we are now able to estimate the Bosporus Strait annual mean netflow.