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Many previous studies on lacustrine basins in the East African Rift System have directed their attention to climatic controls on contemporary sedimentation or climate change as part of palaeoenvironmental reconstruction. In contrast, this research focuses on the impact of tectonism and volcanism on rift deposition and develops models that help to explain their roles and relative importance. The study focuses on the spatial and temporal variability in bulk sediment geochemistry from a diverse range of modern and ancient rift sediments through an analysis of 519 samples and 50 major and trace elements. The basins examined variously include, or have contained, wetlands and/or shallow to deep, fresh to hypersaline lakes. Substantial spatial variability is documented for Holocene to modern deposits in lakes Turkana, Baringo, Bogoria, Magadi and Malawi. Mio‐Pleistocene sediments in the Central Kenya Rift and Quaternary deposits of the southern Kenya Rift illustrate temporal variability. Tectonic and volcanic controls on geochemical variability are explained in terms of: (i) primary controlling factors (faulting, subsidence, uplift, volcanism, magma evolution and antecedent lithologies and landscapes); (ii) secondary controls (bedrock types, rift shoulder and axis elevations, accommodation space, meteoric and hydrothermal fluids and mantleCO₂); and (iii) response factors (catchment area size, orographic rains, rain shadows, vegetation densities, erosion and weathering rates, and spring/runoff ratios). The models developed have, in turn, important implications for palaeoenvironmental interpretation in other depositional basins.