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The catchment and water chemistry of Lake Victoria are greatly influenced by the inflow of rivers and the alternation of the dry and wet seasons. The ecological integrity of the lake has been altered as a result of changes in its physical, chemical, and biological properties resulting from natural and anthropogenic forces. With human population growth, there has been an increase in the multiplicity of activities in the lake basin rendering the lake environmentally unstable.The diversity of the fauna, especially of fish and of the flora declined and the health of the ecosystem deteriorated due to excessive fishing pressure, predation, and competition among introduced species, wetland degradation, poor watershed management and pollution. The nutrient content in Lake Victoria has increased and the consequent eutrophication had a big impact on the biodiversity of the cichlids.Factors that had been affecting Lake Victoria had not impacted the small water bodies in the basin on the same scale. There are several pockets of rare and even extinct species in Lake Victoria that still survive in several ox-bow lakes associated with the extensive wetlands around Lake Victoria. The phytoplankton, zooplankton and fish communities known to be missing in the main lake continued to survive in these minor water bodies. Species still occurring in both habitats exhibit different levels of tolerance to exploitation levels. However, there is no clear policy to conserve the minor water habitats. The paper compares the common taxa in Lake Victoria and the satellite lakes identifying the rare ones in an attempt to mobilize forces to conserve them.