Chemostratigraphic studies on lacustrine sedimentary sequences provide essential insights on past cyclic climatic events, on their repetition and prediction through time. Diagenetic overprint of primary features often hinders the use of such studies for palaeoenvironmental reconstruction. Here the potential of integrated geochemical and petrographic methods is evaluated to record freshwater to saline oscillations within the ancient marginal lacustrine carbonates of the Miocene Ries Crater Lake (Germany). This area is critical because it represents the transition from shoreline to proximal domains of a hydrologically closed system, affected by recurrent emergent events, representing the boundaries of successive sedimentary cycles. Chemostratigraphy targets shifts related to subaerial exposure and/or climatic fluctuations. Methods combine facies changes with δ13C–δ18O chemostratigraphy from matrix carbonates across five closely spaced, temporally equivalent stratigraphic sections. Isotope composition of ostracod shells, gastropods and cements is provided for comparison. Cathodoluminescence and back-scatter electron microscopy were performed to discriminate primary (syn-)depositional, from secondary diagenetic features. Meteoric diagenesis is expressed by substantial early dissolution and dark blue luminescent sparry cements carrying negative δ13C and δ18O. Sedimentary cycles are not correlated by isotope chemostratigraphy. Both matrix δ13C and δ18O range from ca −7·5 to +4·0‰ and show clear positive covariance (R = 0·97) whose nature differs from that of previous basin-oriented studies on the lake: negative values are here unconnected to original freshwater lacustrine conditions but reflect extensive meteoric diagenesis, while positive values probably represent primary saline lake water chemistry. Noisy geochemical curves relate to heterogeneities in (primary) porosity, resulting in selective carbonate diagenesis. This study exemplifies that ancient lacustrine carbonates, despite extensive meteoric weathering, are able to retain key information for both palaeoenvironmental reconstruction and the understanding of diagenetic processes in relation to those primary conditions. Also, it emphasizes the limitation of chemostratigraphy in fossil carbonates, and specifically in settings that are sensitive for the preservation of primary environmental signals, such as lake margins prone to meteoric diagenesis.