ABSTRACT A small, closed, lacustrine system developed during the restraining overstep stages of the Oligocene As Pontes strike-slip basin (Spain). The increase in basin accommodation and the headward spread of the drainage, which increased the water input, triggered a change from shallow, holomictic to deeper, meromictic conditions. The lower, shallow, lacustrine assemblage consists of mudstone–carbonate cycles recording lacustrine–palustrine ramp deposition in a saline lake. High Sr content in some early diagenetic calcites suggests that aragonite and calcite made up the primary carbonate muds. Early dolomitization took place together with widespread pedogenic activity. The upper, deep, freshwater, lacustrine assemblage includes bundles of carbonate–clay rhythmites and fine-grained turbidite beds. Primary calcite and diagenetic siderite make up the carbonate laminae. The Mg content of the primary carbonates records variations in Mg/Ca ratios in lacustrine waters. δ18O and δ13C covariance trends in calcite reinforce closed drainage conditions. δ18O data indicate that the lake system changed rapidly from short-lived isotopically light periods (i.e. from seasonal to pluriannual) to longer steady-state periods of heavier δ18O (i.e. from pluriannual to millennial). The small δ13C changes in the covariant trends were caused by dilute inflow, changing the contributions of dissolved organic carbon in the system and/or internal variations in lacustrine organic productivity and recycling. In both shallow and deep carbonate facies, sulphate reduction and methanogenesis may account, respectively, for the larger negative and positive δ13C shifts recorded in the early diagenetic carbonates (calcite, dolomite and siderite). The lacustrine system was very susceptible to high-frequency, climatically forced water balance variations. These climatic oscillations interfered with the low-frequency tectonic and morphological changes in the basin catchment. This resulted in the superposition of high-order depositional, mineralogical and geochemical cycles and rhythms on the lower order lacustrine infill sequence.