The limnology of Lakes Malawi Tanganyika, and Victoria is discussed with the objective of examining how the physical, chemical, and biological properties of the lakes will determine the response of these ancient great lake ecosystems to human activities. Of the physical properties discussed, large dilution capacities and long flushing times can make the detection and removal of chemical pollutants in these lakes difficult. The outflows of all three lakes are small because of high evaporation losses, and as a result lake levels are responsive to climate changes that would alter evaporation:precipitation ratios. Increased nutrient input to these lakes will likely result in a decrease in the volume of oxygenated water and available fish habitat. Plankton community composition will also change, probably toward dominance by cyanobacteria. While the effects of eutrophication on fish production are difficult to predict, changes in plankton composition would almost certainly be accompanied by changes in fish community structure. Recent studies of water chemistry and plankton productivity in Lake Victoria provide evidence of possible eutrophication. Because land use has a diffuse but potentially large impact on these lakes, conservation strategies must take into account human activities within entire drainage basins. This requires cooperation between riparian countries and technological and financial input from the international community. An immediate need is the establishment of monitoring programs to determine the impact, real or potential, of human activities around the lakes.

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Lake Malawi, an East African Rift Valley lake, is internationally renowned for having the highest diversity of fish species in the world, and these cichlids are highly specialized in their dietary habits. In this lake, tissue stable carbon (delta13C) and nitrogen (delta15N) isotopes can be used over several trophic levels to distinguish those consumers relying upon carbon fixed by either benthic or pelagic primary producers. As such, it was possible to contrast the biomagnification of persistent organochlorines through the benthic and pelagic food webs. In 1996 and 1997, food-web organisms were collected from Lake Malawi and analyzed for organochlorines, delta13C and delta15N to determine the factors that affectthe biomagnification of contaminants in a tropical lake. The pesticide DDT was the most predominant pollutant in the biota from Lake Malawi and was found at the highest concentrations in the largest and fattiest fish species. As observed in temperate systems, log-transformed sigmaDDT concentrations in food-web organisms were significantly predicted by delta15N or log lipid (r2 = 0.32 and 0.40, respectively). In addition, the slope of the regression of log sigmaDDT versus delta15N was significantly higher in the pelagic than the benthic food web. These results indicate that pelagic organisms are at greater risk of accumulating these pollutants than biota relying upon benthic primary production.

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We use historic water temperature measurements to define a deep‐water warming trend in Lake Malawi, East Africa. Over the past six decades, the temperature of the deep water below 300 m has increased by ~0.7°C. The warming trend is due mainly to the reduction of cold‐water deep convection over this period, which is associated with milder winters in the region. Despite deep‐water warming, density stratification was maintained at depths below 100 m. The observed warming trend was interrupted at least twice by abyssal cooling events that were associated with the wettest years on record. We propose that rainfall and cool river inflow are critical factors that control thermal structure and the rate of deep‐water recharge in this deep, tropical lake.

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