Lakes are excellent recorders of long-term changes in soil erosion from river drainages, but in semi-arid tropical regions this record is complicated by the climate-driven effects of basin hydrology on sedimentation. We analyzed a ~21,500-yr record of the rate of sediment accumulation (SAR) in Lake Naivasha (central Rift Valley, Kenya), to provide a long-term perspective for the recently accelerating sedimentation attributed to agricultural soil erosion. Over the whole of post-glacial history, SAR is positively related to lake level with peak values during the early Holocene humid period (~9200 to ~5650 years ago). At this time scale, SAR mainly reflects variations in sediment yield from the landscape as influenced by total rainfall and vegetation type. A very low mean SAR during the arid Medieval Climatic Anomaly indicates that this positive long-term relationship was enhanced by the interruption of lacustrine sedimentation during the driest periods, when the crater basin became isolated from river inflow and complete desiccation caused sedimentary hiatuses due to deflation. In contrast, at decadal time scales over the past century SAR is negatively related to lake level because modest lowstands enhance focusing and re-deposition of shallow-water sediments in deeper areas of the crater. Mean SAR during the period 1900-1960 was only modestly higher than its mean value for the past 750 years, indicating that colonial-time land use around Lake Naivasha did not cause excessive sediment input to the lake. A clear signature of anthropogenic sediment loading (2.5 to 4 times the natural, pre-impact value) is evident only from the early 1990s, coincident with greatly intensified industrial horticulture and large-scale clearance of sediment-buffering papyrus swamp. These results demonstrate the need for a long-term perspective to properly constrain the anthropogenic component of historical SAR variation in fluctuating lakes.