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Climate warming over the 20th century has increased the density stratification and stability of Lake Tanganyika, a deep rift valley lake. Here we examine the physical processes involved in and affected by the warming of the lake, and we discuss effects on lake productivity. The rate of net heat absorption by Lake Tanganyika has been 0.4 W m⁻² since 1913, twice the rate in the global ocean, indicating stronger climate forcing in the East African region. Lakes warm through increased incoming long‐wave radiation. While lakes in general will increase heat outputs in a warming climate, heat outputs will increase more slowly in deeper lakes than in shallower lakes. Temperatures have increased by 0.2°C at 1000 m in depth, in part because of reduced cool marginal inflows, while water surface temperatures have increased by about 1.3°C. This differential heating over depth has increased the density gradient through the …