This study assessed plankton density and biomass in an attempt to better understand their spatial and seasonal variation in Lake Malombe. Samples were collected for analysis during the hot dry season (HDS) and cool dry windy season (CDWS). The zooplankton identified were T. cunningtoni (TC), M. aEq. Aequatorialis (MAA), T. neglectus (TN), Bosmina longirostris (BL), Diaphanosoma spp (DS), Nauplii, and Rotifer. These zooplankton groups belong to copepods, Cyclopidae, Cladocera, Ctenopod, and Rotifers. The phytoplankton biomass exhibited a strong seasonal variation with the highest value observed in HDS and lowest in CDWS. Zooplankton such as T. cunningtoni, M. aEq. Aequatorialis, T. neglectus, Bosmina longirostris, Diaphanosoma spp, Nauplii, and Rotifer were dominant during the HDS. The WT, pH, and DO, Chlo-a positively correlated with all zooplankton groups. The Na+ and K+ positively correlated with TC, MAA, DS, Nauplii, and Rotifers. The Cl− positively correlated with DS, Rotifers while, CO32− positively correlated with TC. HCO3− correlated with DS and Rotifers positively while TDS correlated with BL, Nauplii, and Rotifers negatively. Nitrite affected all zooplankton groups negatively while SRP had a positive effect on all zooplankton density. The study revealed that physical-chemical variables, some major ions, and Chlo-a are the most important factors influencing the spatial and seasonal variation of zooplankton density in the lake. These findings demonstrate the interaction between physical-chemical variables, phytoplankton, and zooplankton and highlight the significance of ecological understanding of the complex dynamics of food web system in tropical shallow lakes - under the changing climate.