The last millennium is a key period for understanding environmental change in eastern Africa, as there is clear evidence of marked fluctuations in climate (effective moisture) that place modern concern with future climate change in a proper context, both in terms of environmental and societal impacts and responses. Here, we compare sediment records from two small, nearby, closed crater lakes in western Uganda (Lake Kasenda and Lake Wandakara), spanning the last 700 (Wandakara) and 1200 years (Kasenda) respectively. Multiproxy analyses of chemical sedimentary parameters (including C/N ratios, 13 C of bulk organic matter and 13 C and 18 O of authigenic carbonates) and biotic remains (diatoms, aquatic macrofossils, chironomids) suggest that Kasenda has been sensitive to climate over much of this period, and has shown substantial fluctuations in conductivity, while Wandakara has a more muted response, likely due to the increasing dominance of human activity as a driver of change within the lake and catchment over