The study was conducted to establish factors that influence phytoplankton diversity community structure in cages and there ecological implications. to human health. Sampling stations were selected in triplicates. Parameters determined include nutrients, phytoplankton chlorophyll and algal toxins. Phytoplankton diversity index was calculated by Shannon Wiener diversity index and phytoplankton richness calculated by Simpson richness Index. Statistical significance was set at p < 0.05. Statistical analysis was performed using Minitab version 17 Inc. for windows. There was a significant difference in chlorophyll a, temperature, dissolved oxygen, conductivity, pH and Secchi depth at Anyanga (ANOVA; p<0.05). However, no significant difference was observed in nutrients measured in Victory farm (ANOVA; P˃0.05). Mean overall dissolved oxygen was 7.41 ± 1.39 mg/l and varied significantly between sampling stations (p = 0.0491). Mean conductivity levels was 142.39 ± 63.786 µS/cm, but differed significantly between stations (p = 0.0005). The mean phosphorus level was 330.02 ± 311.9 mg/l but differed significantly between sampling sites (p = 0.001). The mean overall ammonium level was 319.29 ± 397.35mg/l which was observed have varied significantly between sites (p = 0.0008). The mean overall Chlorophyll a level was 592.9 ± 604.38 mg/ l at Mfangano cages. At 46%, the Diatoms were the most predominant phytoplankton family in the study. There were significant differences in phytoplankton families between stations (p = 0.0001). Besides, the results can be used to rank the cages with respect to levels of pollution. High turbidity negatively affects the lake ecosystem hence proliferation of Cyanobacteria is likely to occur in cages, presently and in future with poor management practices
KEY WORDS: Water Quality, Chlorophyll-a, Phytoplankton abundance, Nutrients, cages Management implications