Lithological and biological features of a fossiliferous tufa in the Kapthurin Formation, Baringo, Kenya, reveal the presence of a lush wetland in a semi-arid environment during the Middle Pleistocene (ca 500 ka) in this portion of the East African Rift Valley. Four geological sections, each between 3 m and 8 m in thickness, exposed over a distance of 0·5 km, reveal a 1 to 2 m thick paludal tufa which is composed of three carbonate beds, two dark grey silty claystones and a reddish-brown silty palaeosol. High resolution stratigraphic analysis, carbonate petrography, stable isotope and elemental geochemistry, clay mineralogy and fossil remains (molluscs, ostracods, diatoms and charophytes) reveal a ground water-fed system that fluctuated in depth and periodically disappeared altogether. Oxygen isotope ratios (δ18O) of tufa matrix range from −4·5‰ to −8·0‰ (Vienna Pee Dee Belemnite) and become more positive up section, indicating the decreasing influence of fault-related fluids and increasing residence time or freshness of wetland water, rather than evaporative enrichment. This spring was situated on a lake margin during low lake levels, thrived during periods of increased ground water input and was ultimately replaced by an alkaline lake. The wetland would appear to have existed during a cool interval within the generally warm Marine Isotope Stage 13 or perhaps during the warm second half of Marine Isotope Stage 13. The ground water source of this wetland arose through a fault system. Thus, the position of the tufa deposit is controlled structurally but the timing and duration of the wetland system may have been influenced by both climatic and tectonic factors.