Diatom dissolution in saline lakes represents an important obstacle to the quantitative reconstruction of water chemistry and climate from lake sediment archives. This problem is here approached experimentally by artificially dissolving diatom-bearing core sediment from Lake Manyara, Tanzania. Manyara holds one of the longest continuous palaeolimnological records from tropical Africa although its interpretation is based on a fragmentary diatom record due to frustule dissolution. These experiments have revealed clear changes in assemblage composition as dissolution operated differentially with respect to diatom taxa. Differential dissolution has considerable impact on the water chemistry estimates derived from transfer functions. Taphonomy, rather than environmental change, may have been responsible for minor fluctuations in the diatom assemblages from Manyara, although major palaeohydrological changes during the Late Pleistocene and Early Holocene can be identified. Particularly well represented by MANE-87 is a period of intermediate lake level between 27 500 and 23 000 14C yr BP which has regional palaeohydrological significance.