Well-dated sediment cores from Lake Tanganyika provide records of environmental change over timescales of centuries to millennia, giving us insights about how this complex ecosystem has responded to processes such as climate change (both before and after the onset of the industrial revolution) and watershed deforestation. They extend our knowledge of changes into the pre-observational era and the period prior to intensive land use, large-scale fishing and anthropogenic warming. The epilimnion of Lake Tanganyika has warmed significantly since the 19th century, causing increased water column stratification, declining internal nutrient loading and primary production, and shoaling of the lakes oxicline, reducing habitable area for benthic and demersal organisms. Simultaneously, nearshore ecosystems have experienced rapid increases in sedimentation from watershed deforestation. The effects of this process have been most strongly felt in regions with large, broad watersheds that feed into relatively gently sloping offshore areas, where increased sediment yields are spread over large regions of high biodiversity. This process is also climate mediated, with periods of extreme precipitation triggering the onset of increased sediment delivery in previously denuded watersheds. Periods of increased precipitation probably also exacerbated the discharge of externally loaded nutrients from population centers and large agricultural operations, particularly in the northern part of the lake basin. Going forward, understanding how these various processes, coupled with others like fishing activity and species introductions, might interact will require a modelling approach that is parameterized by combining short-term observations and long-term paleolimnologic data.