The difficulty of correlating continental deposits hinders predicting lacustrine and palustrine carbonate facies variations in time and space. This study aims to understand better the factors governing these facies heterogeneities by measuring carbonate isotopes and conducting facies, petrographic and sequence stratigraphic analyses of the Lutetian–Aquitanian deposits of the Paris Basin, that record the transition from marine to lacustrine environments. Large‐scale correlations enabled the definition of two lacustrine–palustrine carbonate facies models. (1) The coastal lacustrine system (Bartonian to Rupelian), consists of fine‐grained brackish carbonate exhibiting episodic marine inputs during short‐term relative sea‐level maxima and evaporite sedimentation during relative sea‐level minima. Lacustrine sediments differ notably from marine ones with more negative δ13C and δ18O compositions that co‐vary and a biota adapted to low salinity conditions. In the associated palustrine environment, depositional sequences evolve upwards from micritic lacustrine deposits to nodular and then laminar calcretes. Microbial‐coated grains and rhizoliths indicate biological processes during repeated subaerial exposure phases in sub‐tropical to arid climates. (2) The inland lacustrine system (Rupelian and Aquitanian) was disconnected from the marine domain and showed evidence of microbial activity with microbial crusts and oncoidal rudstones. Facies rich in micritic intraclasts composed of palustrine and lacustrine facies indicate the reworking of already lithified sediments along the margins. In the palustrine domain, the calcrete facies are less abundant than breccias formed in‐situ by desiccation, limestones with root traces, or organic‐rich wackestones and marls. This system reflects a more temperate climate with more developed microbial structures and less exposed carbonates than the coastal lacustrine system. The southward migration of the depocentre and the transition from marine environments to (1) coastal and then (2) inland systems are controlled by uplift phases induced by Pyrenean and Alpine orogenesis. Third‐order relative sea‐level variations appear to control only short‐term cycles in coastal systems.