Loboi Swamp is a 1·5 km2 freshwater wetland situated near the equator in the Kenya Rift Valley. The climate is semi-arid: precipitation is ≈ 700 mm year−1, and evapotranspiration is ≈ 2500 mm year−1. Some of the wetland water is currently used for irrigation. An interdisciplinary study was conducted on the geology, hydrology, pedology and biology of the wetland to determine its origin and history and to assess its longevity under present hydrological conditions. Sedimentary records from two piston cores (1·8 and 4 m long) indicate that the present wetland developed during the late Holocene on a low-relief alluvial plain. Floodplain deposits (sandy silts) are capped with wetland sediments (organic-rich clay and peat), which began to form at ≈ 700 BP. The swamp is dominated by Typha domingensis Pers. (≈ 80%) and floating Cyperus papyrus L. (20%). It is fed by warm springs (T ≈ 35 °C; pH ≈ 6·4–6·9) emanating from grid faults of the rift floor. Water compositions suggest that sources are dominated by shallow meteoric water, with little contribution from deeper geothermal fluids. Siderite concretions in the floodplain silts reflect the Fe-reducing conditions that developed as the surface became submerged beneath the water table. The pollen record captured both local and more regional vegetation, showing the prevailing dry rift valley climate despite development of the wetter conditions on the valley floor. The diatom record also suggests a dramatic change in local hydrology. The combined biological records of this semi-arid wetland indicate an abrupt change to wetter conditions, most probably as a result of a regional change in climate. Rift tectonics provided accommodation space, maintained the wetland at or below the water table and enabled spring recharge. The size of the modern wetland has been reduced by about 60% since 1969, which suggests that the system may now be under hydrological stress due to anthropogenic impacts from land-use change.