Lake Turkana and Lake Naivasha are two freshwater lakes in the Kenyan Rift Valley that differ significantly in water chemistry and anthropogenic influence: Lake Turkana is believed to be rather pristine and unpolluted, but a previous study has shown rather high levels of Li, Zn, and Cd in the migratory fish species Hydrocynus forskahlii, questioning this pristine status. Lake Naivasha is heavily influenced by agricultural activity in its catchment area and by direct water use, and high levels of metal pollutants have been reported in fish. This study presents the distribution of nine important trace elements in liver and muscle of the nonmigratory red belly tilapia Tilapia zillii from Lake Turkana and from Lake Naivasha (before and after a significant rise in water level due to as yet not fully understood reasons). In addition, trace element levels in the common carp Cyprinus carpio from Lake Naivasha are presented. Metal concentrations measured in the liver and muscle of T. zillii collected in Lake Turkana confirm the pristine status of the study site, but contrast with the results obtained for the migratory H. forskahlii. Comparing T. zillii from the two lakes reveals a clear difference in accumulation patterns between essential and nonessential trace elements: physiologically regulated essential elements are present in a very similar range in fish from both lakes, while levels of nonessential metals reflect short- or long-term exposure to those elements. The comparison of trace element concentrations in the fish samples from Lake Naivasha showed lower levels of most trace elements after the significant increase of the water level. This study demonstrates that fish are valuable bioindicators for evaluating trace element pollution even in contrasting lakes as long as the way-of-life habits of the species are taken into account.