Fossil and living stromatolites are abundant around the margins of Lake Tanganyika, Africa, and provide a wealth of paleolimnologic and paleoclimatic information for the late Holocene. Six lines of evidence show that stromatolites and cements are precipitating in the lake today: (1) carbonate saturation state calculations, (2) documentation of living stromatolites and their depth distribution, (3) new stable isotope data showing the lake’s present mixing state and ancient evaporation and inflow balance, (4) new radiocarbon data and a reevaluation of apparent 14 C ages derived from Lake Tanganyika carbonates, (5) the presence of modern Mg-calcite cements derived from lake waters, and (6) the presence of modern, biologically mediated Mg-calcite precipitates in the lake. Lake Tanganyika’s lake levels have been remarkably stable over the past 2800 yr, fluctuating around the marginally open to marginally closed level through most of this time period. Lake lowstands and high δ 18 O values from the ninth century B.C. to the early fifth century A.D. indicate that the lake basin was comparatively dry during this time. However, the period prior to the most recent opening of Lake Kivu into the Lake Tanganyika basin (ca. A.D. 550) was not marked by major lake lowstands, nor was this opening accompanied by a dramatic lakelevel rise. The Kivu opening was roughly coincident with a significant shift toward isotopically lighter (δ 18 O and δ 13 C) lake water, which persists today. The lake remained close to its outlet level between the sixth and thirteenth centuries A.D. Lake levels rose between the fourteenth and sixteenth centuries. At some time between the late sixteenth and early nineteenth centuries, lake level fell to perhaps its lowest level in the past 2800 yr. By the early nineteenth century, lake level had begun to rise to the overflow level, apparently the result of a regional increase in precipitation/evaporation ratios. Weak δ 18 O/δ 13 C covariance for late Holocene carbonates suggests that the surface elevation of the lake has remained near the outlet level, with only occasional periods of closure. However, there is no simple relationship between solute input from Lake Kivu, isotope input from Lake Kivu, and lake levels in Lake Tanganyika. Lake Kivu waters are the primary source of major ions in Lake Tanganyika, but are much less important in controlling the δ 18 O and the lake level of Lake Tanganyika. Because the Ruzizi River’s discharge into Lake Tanganyika is largely derived from sources other than Lake Kivu, the overflow events in the two lakes have been uncoupled during the late Holocene.