Spatial patterns and abundance of zooplankton in aquatic habitats are important determinants for production of fish species, invertebrates and availability of phytoplankton. Weekly monitoring for zooplankton abundance was conducted in Shirati Bay, Lake Victoria, to explore their spatial patterns in relation to phytoplankton, fish catch and some water quality parameters. The vertical distribution of zooplankton was generally higher close to the bottom as compared to surface waters of the lake. Zooplankton vertical distribution positively correlated with water transparency (r = 0.680, p = 0.011). The horizontal abundance of zooplankton was not significantly different amongst the three stations (p = 0.5143). While Copepoda was the dominant group in terms of composition, Rotifera had the highest diversity indices of all the zooplankton groups obtained. The abundance of nauplius larvae was significantly higher than that of the copepodites (p = 0.022). Nile perch, Lates niloticus dominated the total catches (47%) followed by Nile tilapia, Oreochromis niloticus (29%) and haplochromines (21%). The abundance of haplochromines and juvenile fishes correlated significantly with the abundance of zooplankton (r = 0.856, p = 0.002 and r = 0.58, p = 0.038, respectively). The current study revealed that zooplankton vertical distribution at Shirati Bay is mainly controlled by water transparency and predation by juvenile Nile perch, Nile tilapia and haplochromines.