There is a paucity of long and continuous continental records from South East Asia suitable to inform on past changes and underlying causes of the region's climate and associated diverse ecosystem evolution during the late Quaternary. In 2015, the Towuti Drilling Project (TDP) collected a series of sedimentary drill cores from the tectonic, ferruginous, and highly biodiverse Lake Towuti, Sulawesi, one of Indonesia's oldest lakes. The drill cores contain ~1 Myr of uninterrupted lacustrine sedimentation to document long-term environmental and climatic change in the tropical western Pacific, the impacts of geological and environmental changes on the biological evolution of aquatic taxa, and the geomicrobiology and biogeochemistry of metal-rich, ultramafic-hosted lake sediment. Here we use lithostratigraphic, mineralogical, geochemical, and geochronological datasets to elucidate Lake Towuti's tectonic emergence and its biogeochemical responses to climatic and volcanic forcings since lake formation. Our data document that Lake Towuti emerged during a phase of accelerated tectonic subsidence from a landscape characterized by active river channels, shallow lakes and swamps into a permanent lake at ~1 Ma. The lacustrine sediments feature quasi-rhythmic alternations of green organic rich and red sideritic clay beds reflecting changes in lake mixing and biogeochemistry as a response to temperature and hydrological changes driven by orbital-scale changes in insolation and continental ice volume through the mid- to late Pleistocene. Clay deposition is interrupted by two beds of diatomaceous oozes composed primarily of planktonic diatoms that reflect phases of substantially increased primary productivity. The occurrence of these diatomaceous oozes in close association with multiple tephra beds suggests a trophic state change driven by the addition of volcanically sourced P, possibly in combination with a lake mixing state that supports recycling of P. Data on lake age and ontogeny are also in agreement with molecular-clock estimates of ~0.7 Ma (0.18-1.37 Ma) for the divergence of Lake Towuti's Telmatherinid fishes from a riverine ancestor. Our data therefore are compatible with an evolutionary model in which Lake Towuti's endemic fauna is a result of geographic speciation in the Malili Lakes, a set of large lakes in Southeast Sulawesi, driven by physical or chemical dispersal limits imposed by the regional rivers and lakes. More detailed chronological constraints and refined climate and environmental proxy datasets are currently in preparation and will help to paint a more detailed history of the region's climate and environmental history in future studies.