Freshwater aquatic ecosystems are continuously exposed to increasing threats from anthropogenic activities, climate change and the expanding urban population. There is no long-term data and information to understand the effects of urbanization and watershed nutrient sources, on the ecological health of the several shallow embayments. This study explored the changes in environmental conditions and influences on fish species composition and distribution, using data collected between 2018 to 2024 (Dry and wet seasons) in Kisumu bay. Over the seven years, the water temperature, turbidity, salinity, total dissolved solids, conductivity, dissolved oxygen, oxygen reduction potential, pH and Secchi depth revealed significant variations (p < 0.05) between the years, stations and sampling months. In 2023, a lower mean turbidity and higher conductivity, increased light transparency was recorded than the previous years in areas which are within the inner zone of the bay. Significant seasonal variations (p < 0.05) were evident for the measured turbidity, secchi depth and water temperature. Over the three years (2022-2024) nutrient elements varied significantly but differently across the years, stations and zones; except for dissolved silicon. The mean phytoplankton biomass (Chlorophyll-a) was 104.19±150.20 ugL-1 and the lake water exhibited eutrophic to hypereutrophic conditions. The two introduced fish species (Lates niloticus and Oreochromis niloticus) and the endemic Haplochromines and Synodontis victoriae were the dominant fish species. Watershed management and efficient waste management are a priority for reduction of soil erosion and control of diffuse pollution sources; and protection of the natural aquatic habitats.
