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The heterogeneous ecosystems in the Mediterranean Basin (MB) are becoming sensitive to water stress. To investigate the climatic stress, a water budget study was conducted over the basin using TerraClimate simulations for a long temporal range (1990–2020). According to the budget accounting, forested regions received the highest precipitation (P) on average compared to other land use types (annual mean ≈633 mm yr−1), and even then, they were in a water deficit state (−0.42 mm yr−1). Tree plantations in North Africa (Libya and Morocco) were also in a water deficit state; however, their average P was very low (≈12 mm yr−1) compared to that of northern parts of the MB, and the average Actual Evapotranspiration (AET) was ≈15 mm yr−1. Also, the water balance in other land use systems (rain-fed, irrigated croplands, and rangelands) was either negative or near zero. As a whole, the basin's average annual P was ≈538 mm yr−1, the annual average AET was ≈415 mm yr−1, and the runoff (Q) was equivalent to 123 mm yr−1, which shows a strong influence of ET over the region. Since runoff was negligible in most dry areas, the AET's large contribution was notable in the North African base of the Atlas Mountains including the Nile delta region. This indicates that precipitation and evaporation are the principal mechanisms of the water balance in the MB. The result shows strong climate variability over Southern Europe, Turkey, and the western Balkans in the recent years, affecting the AET and making their land use systems more vulnerable to water stress. This benchmark study signifies the consistent need for water storage in the Mediterranean vegetation systems of the basin. It also indicates two distinct climate clusters for water balance modeling. [ABSTRACT FROM AUTHOR]