During the past decades, major anthropogenic environmental changes occurred in Lake Victoria, including increased predation pressure due to Nile perch introduction, and decreases in water transparency and dissolved oxygen concentrations due to eutrophication. This resulted in a collapse of the haplochromine cichlids in the sub-littoral waters of the Mwanza Gulf in 1986-1990, followed by a recovery of some species in the 1990s and 2000s, when Nile perch densities declined. We studied two data sets: (1) haplochromines from sand and mud bottoms in the pre-collapse period; (2) haplochromines from sub-littoral areas during the precollapse, collapse and recovery periods. Water over mud is murkier and poorer in oxygen than water over sand, and differences in haplochromine communities in these natural habitats during the pre-collapse period may predict the effects of anthropogenic eutrophication during the collapse and recovery periods. In the pre-collapse period, haplochromine densities over sand and mud did not differ, but species richness over sand was 1.6 times higher than over mud bottoms. Orange-and white-blotched colour morphs were most common at the shallowest sand station. More specifically, insectivores and mollusc-shellers had higher numbers of species over sand than over mud, whereas for mollusc-crushers no difference was found. Laboratory experiments revealed that mollusc shelling was more affected by decreased light intensities than mollusc crushing. During the pre-collapse period, spawning occurred year-round in shallow areas with hard substrates and relatively clear water. In deeper areas with mud bottoms, spawning mainly occurred during months in which water clarity was high. No effects of hypoxia on spawning periods were found. It follows that clearer water seems to support differentiation in feeding techniques as well as year-round spawning, and both may facilitate species coexistence. Water clarity is also known to be important for mate choice. These observations may explain why, since the decline of Nile perch, haplochromine densities have recovered, the numbers of hybrids increased and species diversity in the current eutrophic sub-littoral waters has remained 70 % lower than before the environmental changes.