Lithofacies analyses were undertaken on a suite of well-exposed carbonate deposits from the (Pliocene) Mayrán Formation, in the Mayrán Basin system, northeast Mexico to investigate the controls on carbonate lithofacies variability in a series of linked lacustrine subbasins, with a common hydrology yet very different inputs. The lacustrine carbonates contain variable proportions of production-derived components, with subordinate proportions of detrital and early diagenetic components. The lithofacies contain, inorganic and organic calcite (average 91% CaCO3), and organic matter (10.5%–13.8% average 12.6% TOC), together with minor detrital minerals. Nine sub-facies were identified: ostracod mudstone-wackestone, clotted boundstones, gastropod wackestone-packstones, oncoid wackestone-packstones, charophyte wackestone-packstones, crystalline carbonate mudstone, stromatolites, crystalline carbonate, marlstone, and associated evaporite minerals. Isotopic composition of specific components such as micritic laminations in stromatolites (δ13Ccalcite −6.3‰ and δ18Ocalcite −8.0‰), and micrititic matrix from samples in all the subbasins (δ13Ccalcite −5.7‰ and δ18Ocalcite −7.8‰), indicate that overall calcite deposition occurred in freshwater lakes. Non luminescent (e.g. charophytes) to orange dull luminescencent micrite strongly suggest in situ carbonate production. Together these processes contributed to the local production of lime mud. Additionally, microtextural evidence of scour surfaces however, indicates that occasionally the sediment was reworked and transported laterally and basinward. Fossil content and diversity composed by Limnaeidae, Physidae, and Planorbidae types, together with phosphatised bone fragments, micro-oncoids, stromatolites, microbial morphotypes, charophytes, macrophyte phytoherms, and microcodium structres, are good references for lithofacies characterization and indicators of specific paleoenvironmental conditions. Intense to moderate bioturbation (BI 1 to 4), indicates that deposition took place under predominantly oxic conditions. Significant organic matter was preserved in these lacustrine rocks, likely controlled by moderate rates of carbonate mud production. The lacustrine lithofacies were deposited in proximal and distal lacustrine settings, making possible to recognize basin scale variability. Strata staking patterns are organized into shallowing upwards cycles (0.3–2.5 m thick), which are capped either by evaporites or beds with a pedogenic overprint. Their stacking patterns reflect lake level variations which can be recognized in all the subbasins. The lithofacies architecture within each subbasin forms parasequences that overall exhibit aggradational geometries. The lithofacies and their large scale geometries also indicate deposition occurred in a series of relatively shallow (<10 m), lake systems with ramp-like margins. The aggradational stacking patterns of the carbonates and the presence of subordinate evaporites suggest that basin hydrology (water supply and precipitation/evaporation ratios) had an important influence on facies architecture and cyclicity. The Mayrán Formation lacustrine lithofacies deposited under overfilled to balance-filled lake conditions; although balance-filled conditions with an open hydrology were more likely. Overall, facies variability in the lacustrine carbonate lithofacies was controlled by basin inherited geomorphology, accommodation, and basin hydrology, which ultimately controlled clastic trapping, solute inputs, water chemistry, primary production, and lake level changes. We interpret that all these controls were largely driven by climate.