Geochemical data from drill cuttings of a 3,392 m deep well drilled on the shores of Lake Albert-Uganda, East Africa were used to investigate a longterm paleoenvironmental history of the Lake Albert rift basin-Uganda. The Ngassa-2 well was drilled through loose and coarse-grained sands in the upper section, massive mudstone deposits interbedded with siltstones in the middle sedimentary section, and a thin conglomerate at the base. Statistical treatment of data by using Principal Component Analysis shows that Fe, Ti and Rb (silicate mineral elements) account for much of the variability in the data, with about 40% of the total variance compared to 20% for total organic carbon (TOC) and Si (organic and quartz). Results from XRF data and TOC are indicative of warm and wet conditions around the late Miocene, later developing into cooler and dryer climatic conditions around the late Pliocene. Anoxic lacustrine conditions in the early Pliocene are documented by a dramatic rise in TOC and coinciding trends with iron for the depth interval 3,000–3,250 m. Lithological observations, seismic data attributes, and down-hole gamma ray logs provide evidence of a basin that transitioned from fluvial to mixed fluvial-lacustrine and subsequently dominantly lacustrine environment before shifting back to fluvial and shallow lacustrine system in the late Pleistocene and Holocene.