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%).