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An integrated ecohydrological modeling approach was deployed in three long‐term critical zone (CZ) observatories of the French CZ network (CZ Observatories—Application and Research) to better understand how the CZ heterogeneity modulates the water cycle within territories. Ecohydrological simulations with the physically based model EcH2O‐iso constrained by a wide range of observations crossing several disciplines (meteorology, hydrology, geomorphology, geophysics, soil sciences, and satellite imagery) are able to capture stream water discharges, evapotranspiration fluxes, and piezometric levels in the Naizin, Auradé, and Strengbach watersheds. In Naizin, an agricultural watershed in northwestern France with a schist bedrock underlying deep weathered materials (5–15 m) along gentle slopes, modeling results reveal a deep aquifer with a large total water storage (1,080–1,150 mm), an important fraction of inactive water storage (94%), and relatively long stream water transit times (0.5–2.5 years). In the Auradé watershed, representative of agricultural landscapes of the southwestern France developed on molasse, a relatively shallow regolith (1–8 m) is observed along hilly slopes. Simulations indicate a shallow aquifer with moderate total water storage (590–630 mm), an important fraction of inactive water storage (91%), and shorter stream water transit times (0.1–1.3 years). In the Strengbach watershed, typical of mid‐mountain forested landscapes developed on granite, CZ evolution implies a shallow regolith (1–5 m) along steep slopes. Modeling results infer a shallow aquifer with the smallest total water storage (475–575 mm), the shortest stream water transit times (0.1–0.7 years), but also the highest fraction of active water storage (18%). Plain Language Summary: Understanding how water is stored and released in landscapes is essential for predicting water availability in a changing world. It is of course driven by the local climate, but also by the landscape settings, from the vegetation to the belowground structure inherited from the geological history. In three intensively studied observatories across France, we used numerous field measurements and a numerical model of water‐vegetation‐subsurface interactions to better depict how differences between landscapes shape the water cycle. We found that the geological history determines how much water is stored in watersheds, through the thickness of water‐holding rocks and soils. How this storage contributes to surface processes (including river flow) is modulated by more recent changes, from valley morphology and tectonics to agricultural practices and precipitation patterns. This study highlights that considering the continuity between long and short‐term landscape processes is key to a detailed understanding of the water cycle. Key Points: The long‐term critical zone (CZ) evolution controlling the regolith thickness strongly impacts the total water storage in watersheds, while the Quaternary geomorphological evolution influences the current hydrological partitioning and the separation of hydrologically active and inactive water storageBoth internal watershed characteristics and external forcings, such as current atmospheric forcing and recent land use need to be considered to infer stream persistence and to understand hydrological diversityThe observed hydrological diversity cannot be fully understood without considering a continuum of time scales in CZ evolution [ABSTRACT FROM AUTHOR]