A small number of ancient lakes (mostly >106 y old) scattered around the globe contain an extraordinary percentage of the world's documented freshwater biodiversity. Endemic benthic invertebrates and fish in most of these lakes today face a variety of anthropogenic threats, including damaging fishing activities, water pollution, species introductions and translocations, climate change, and watershed disturbances. Lake Tanganyika, one of the oldest and most diverse of the ancient lakes, provides a model for studying the effects on endemic faunal diversity from watershed disturbances caused by deforestation. Increased erosion rates around the northern portion of the lake are associated with substantially lower diversity levels for both benthic invertebrates and fish. Disturbance processes in the biologically complex littoral region of this lake that are related to this excess siltation include reductions in light penetration (affecting algal habitat and herbivory), reductions in habitat heterogeneity, and reduced connectivity between benthic habitat patches. Paleoecological data for readily fossilized taxa may be used in Lake Tanganyika to determine background levels and variability in diversity and the historical relationship between human activities in the watershed and changes in benthic community structure. Biogeographic and paleoecologic studies of endemic ostracodes demonstrate that many taxa have extremely patchy distributions which are consistent with metapopulation models of organization. The extremely high diversities encountered in Lake Tanaganyika and other ancient lakes may be dependent on nonequilibrium interactions between patchily distributed species, which undergo periodic but uncorrelated extinctions and recolonizations of appropriate habitat patches. Conversely, excess sedimentation along rocky coastlines may reduce habitat patch interconnections and lead to local extinctions, even in areas that are not directly affected by damaging siltation. Paleoecological data may be used by aquatic conservation biologists to determine the history of this and similar problems and, more generally, to obtain a dynamic view of diversity change in lakes through time.