In impact crater lakes, the lacustrine sedimentary records may not solely reflect climatic changes but also potential erosional effects from lithologically distinct impactite formations. The hydrochemical and biogeochemical processes during the deposition of the Nördlinger Ries impact crater lake, which fall in the range of the mid-Miocene Climate Transition, were studied by analysing microcrystalline authigenic carbonates in a drill core succession, using stable oxygen and carbon isotopes in conjunction with biomarkers. These investigations revealed an early sulfidic interval characterized by thiophenes, iso- and anteiso-C15:0 acids derived from sulfate reducing bacteria, and dolomites with low to intermediate δ13Ccarb values. The subsequent distinctive interval is characterized by extremely 13C-enriched dolomite (δ13Ccarb up to +20.93 ± 0.05‰ V-PDB), decline of iso- and anteiso-C15:0 acids and is rich in an Archaea-derived archaeol that is 13C-enriched (−14.7‰), indicating extensive methanogenesis in sulfate-depleted lake porewater during early diagenesis. The sulfate decline results from successive sulfate reduction when replenishment by sulfate-bearing inflow water is limited. The carbonates exhibit enriched 18O due to pronounced evaporation in a long-resided water body and enriched 13C by methanogenesis. A change in provenance of water derived from the sulfur-rich suevite (impact melt-bearing breccia) and crystalline source rocks to the sulfur-poor Bunte Breccia (continuous ejecta blanket) is required. Intermittently high Si/Al and Zr/Al at the high δ13C interval suggests sporadic short-term runoff increase, leading to fluctuating physiochemical lake conditions. A subsequent decline in both δ13Ccarb and archaeol indicates a decreasing lake level with intermittent subaerial exposure events, supported by bioturbation and mud cracks. The concomitant lake oxygenation is well supported by increasing Pr/Ph ratios and lipids derived from aerobic methanotrophs (13C-depleted 3-methyl-hopanoids). In the youngest unit, allochthonous lignites and biomarkers from lacustrine/soil sources appear, high total sulphur contents and thiophenes recur, and stable C and O isotope values decrease again. These observations suggest another major provenance change of the inflowing solutes, with increasing influx from weathered pyrite-bearing Jurassic claystones. These findings demonstrate that the climatic record expected from the stable carbon and oxygen isotopes of the Ries carbonates is strongly overprinted by hydrochemical and biogeochemical processes due to changing ion influx from substrate rocks, along the course of the successive ejecta erosion and catchment changes. Such an intrinsic control of lacustrine biogeochemical processes is also expected for other hydrologically closed impact crater lake basins, where catchment rocks with distinctively different lithologies are present.