A 50 m thick stratigraphic section at Ngira, near Karungu on the shore of Lake Victoria in western Kenya, documents the early Miocene paleoenvironments of the area. The basal Ngira paleosol is a 7.6 m thick, oxisolic Vertisol that formed during a prolonged period of pedogenesis; it began as a smectite-dominated Vertisol that was later overprinted through polypedogenesis to become a kaolinitic paleosol highly depleted of all base cations, with abundant Fe concentrations and depletions, and complexly variegated color mottle patterns that reflect extensive ferruginization. Paleoenvironmental reconstructions using bulk geochemistry indicate warm and wet conditions during development of the Ngira paleosol that probably supported a tropical seasonal forest on a stable upland surface for 10s to 100s of thousands of years. Following this long-lived stable landscape, rapid subsidence, perhaps associated with slip on a high-angle fault associated with the onset or progression of the Nyanza Rift and/or the development and eruptive history of the nearby Kisingiri volcano, buried the paleosol and formed a nascent lake basin that experienced multiple transgressions and regressions. During one interval of regression, fluvial sandstones and conglomerates were deposited along with fluvio-lacustrine sandstones and claystones that include weakly developed paleosols. These weakly-developed paleosols indicate a relatively dry paleoenvironment with seasonal precipitation, and probably a shrubland/bushland or riparian forest habitat. Important terrestrial and aquatic vertebrate fossils are primarily preserved within fluvial and fluvio-lacustrine deposits, indicating that the terrestrial Karungu fauna lived in a relatively dry and open habitat. This study demonstrates polypedogenesis and inferences regarding onset of abrupt tectonic activity in the early Miocene in equatorial eastern Africa, and emphasizes the contrasts between landscape stability of the Ngira paleosol and the poorly developed soils in the fluvio-lacustrine facies.