Socio-ecological stresses currently affecting the semi-arid regions of equatorial East Africa are driving environmental changes that need to be placed in a proper context of long-term human-climate-landscape interaction. Here we present a detailed reconstruction of past human influences on the landscape of the central Kenya Rift Valley, against the backdrop of natural climate-driven ecosystem dynamics over the past 1300 years. Proxy records of vegetation dynamics (pollen), animal husbandry (fungal spores), biomass burning (charcoal) and soil mobilization (clastic mineral influx) extracted from the continuous depositional archive of Lake Bogoria reveal six distinct phases of human activity. From ca 700 to 1430 CE, strong primary response of savanna woodland ecotonal vegetation to climatic moisture-balance variation suggests that anthropogenic influence on regional ecosystem dynamics was limited. The first unambiguous ecological signature of human activities involves a mid-15th century reduction of woodland/forest trees followed by the appearance of cereal pollen, both evidence for mixed farming. From the mid-17th century, animal husbandry became a significant ecological factor and reached near-modern levels by the mid-19th century, after severe early-19th century drought had substantially changed human-landscape interaction. A short-lived peak in biomass burning and evidence for soil mobilization in low-lying areas of the Bogoria catchment likely reflects the known 19th-century establishment of irrigation agriculture, while renewed expansion of forest and woodland trees reflect the return of a wetter climate and abandonment of other farmland. Since the mid-20th century, the principal signature of human activity within the Lake Bogoria catchment is the unprecedented increase in clastic sediment flux, reflecting widespread soil erosion associated with rapidly intensifying land use.