The Early Cretaceous breakup of Gondwana gave rise to a series of rift basins along the conjugate margins of the South Atlantic, which hosted deep, long-lived paleolakes analogous to the modern East African Rift system. The continuous lacustrine sedimentary successions preserved in these rift basins provide exceptional archives for deciphering aquatic ecosystem responses to rift evolution and extreme climatic or tectonic events over multimillion-year timescales. In this study, we present a multiproxy analysis, including bulk organic carbon isotopes, thermochemical properties, and biomarker distributions, from a drillcore retrieved from the Gabon Basin (West Africa), spanning the Hauterivian to Aptian stages. Our results demonstrate that an initially strongly stratified water column, accompanied by photic‑zone euxinia, was rapidly destabilized during the early phase of rift expansion. We attribute this disruption to basin widening and lake shallowing, which enhanced vertical mixing of the surface water column and thus suppressed persistent anoxia. Beyond these secular shifts in water‑column chemistry, microbial community structures, as reflected in the relative abundances of eukaryotic and bacterial biomarkers, exhibit pronounced rhythmic oscillations with periodicities of 1–2 million years, suggesting a strong external forcing, most likely mediated by orbitally paced hydrological cycles. Collectively, these findings place new quantitative constraints on the lacustrine carbon cycle and its coupled response to tectonic subsidence, basin morphology, and regional hydroclimate. Our study thus offers novel perspectives on the intricate tectonics–environment–carbon feedbacks operating during the nascent stages of Gondwana fragmentation.