Basin hydrology and subcrop are key controls on carbonate sedimentation in continental basins. Hydrologically sensitive carbonates can record groundwater fluctuations within an aquifer in deep time. Late Jurassic extension, footwall uplift, erosion and karstification of marine Jurassic carbonates in the western Cameros Basin (Spain) saw deposition of ?Upper Kimmeridgian‐Tithonian syntectonic alluvial fan deposits (Señora de Brezales Formation). Biogenic laminar calcretes and phreatophytic rhizocretions record roots exploiting capillary fringe groundwater. Progressive infill of rift topography and footwall erosion lowered sedimentary gradients and clastic supply during deposition of the ?Tithonian–Berriasian Rupelo Formation. Distal alluvial marls (Las Viñas Member) contain charophytes, with 2 m thick carbonate lenses at the top reflecting intermittent rise of groundwater in ponds on the basin floor. Stacked palustrine limestones with rare charophytes and laminar calcretes (Ladera Member) record overstep of seasonal carbonate wetlands onto basin margins and footwall highs with intense pedogenetic modification during lengthy seasonal exposure. Overlying Berriasian charophyte‐ostracod wackestones, displaying microkarst cavities and interbedded intraclastic conglomerates, with vivianite sauropod bones, footprints and polygonal desiccation cracks at the top (Mambrillas de Lara Member) record open lacustrine conditions with limited subaerial exposure and high water tables. Desiccation‐cracked limestones and marls with correlatable evaporite horizons (Rio Cabrera Member) contain marginal marine foraminifera and dasycladaceae at the top. Lagoonal conditions reflected transgression to seaward and intermittent marine connection via the Basco‐Cantabrian Basin. The distribution and thicknesses of hydrologically sensitive carbonates reflected onlap onto a faulted and karstified marine Jurassic carbonate pediment and the subtle influence on hydroperiod of fault (and potentially localised Triassic salt) controlled differential subsidence and transgressive groundwater rise. Hydrological facies evolution reflects progressive basin infilling and eustasy beyond. Transitions in this continental succession from clastic to carbonate facies and from closed to open hydrology record hydrological change over time rather than contemporaneous deposition under Walther's Law.