Equatorial East Africa has a complex regional patchwork of climate regimes, sensitive to climate fluctuations over a variety of temporal and spatial scales during the late Holocene. Understanding how these changes are recorded in and interpreted from biological and geochemical proxies in lake sedimentary records remains a key challenge to answering fundamental questions regarding the nature, spatial extent and synchroneity of climatic changes seen in East African palaeo-records. Using a paired lake approach, where neighbouring lakes share the same geology, climate and landscape, it might be expected that the systems will respond similarly to external climate forcing. Sediment cores from two crater lakes in western Uganda spanning the last ~1000 years were examined to assess diatom community responses to late Holocene climate and environmental changes, and to test responses to multiple drivers using redundancy analysis (RDA). These archives provide annual to sub-decadal records of environmental change.

Lakes Nyamogusingiri and Kyasanduka appear to operate as independent systems in their recording of a similar hydrological response signal via distinct diatom records. However, whilst their fossil diatom records demonstrate an individualistic, indirect response to external (e.g. climatic) drivers, the inferred lake levels show similar overall trends and reflect the broader patterns observed in Uganda and across East Africa. The lakes appear to be sensitive to large-scale climatic perturbations, with evidence of a dry Medieval Climate Anomaly (MCA; ca. AD 1000–1200). The diatom record from Lake Nyamogusingiri suggests a drying climate during the main phase of the Little Ice Age (LIA) (ca. AD 1600–1800), whereas the diatom response from the shallower Lake Kyasanduka is more complex (with groundwater likely playing a key role), and may be driven more by changes in silica and other nutrients, rather than by lake level. The sensitivity of these two Ugandan lakes to regional climate drivers breaks down in ca. AD 1800, when major changes in the ecosystems appear to be a response to increasing cultural impacts within the lake catchments, although both proxy records appear to respond to the drought recorded across East Africa in the mid-20th century.

The data highlight the complexity of diatom community responses to external drivers (climate or cultural), even in neighbouring, shallow freshwater lakes. This research also illustrates the importance of, and the need to move towards, a multi-lake, multi-proxy landscape approach to understanding regional hydrological change which will allow for rigorous testing of climate reconstructions, climate forcing and ecosystem response models.