This study assessed zooplankton density and Chl-a amount to 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 Tropodiaptomus cunningtoni (TC), Mesocyclops aequatorialis aequatorialis (MAA), Thermocyclops neglectus (TN), Bosmina longirostris (BL), Diaphanosoma spp. (DS), and Nauplii. These zooplankton groups belong to copepods, Cyclopidae, Cladocera, Ctenopod, and Rotifers. Chl-a exhibited a substantial seasonal variation, with the highest concentration observed in HDS and lowest in CDWS. Zooplankton such as T. cunningtoni, M. aeq. aequatorialis, T. neglectus, B. longirostris, Diaphanosoma spp, Nauplii, and Rotifer increased during the HDS. The water temperatures (WT), pH, Dissolved Oxygen (DO), and Chl-a positively correlated with all zooplankton densities. Sodium (Na þ ) and Potassium (K þ ) ions positively correlated with TC, MAA, DS, Nauplii, and Rotifers. Chloride ion (Cl -) positively correlated with DS, Rotifers, while Carbonate ion (CO 3 2-) positively correlated with TC. Bicarbonate (HCO 3 -) correlated positively with DS and Rotifers, while TDS correlated negatively with BL, Nauplii, and Rotifers. Nitrite affected zooplankton density negatively, while SRP had a positive effect. The study revealed that physical-chemical variables, some significant ions, and Chl-a are the most critical factors influencing the spatial and seasonal variation of zooplankton density in the lake. These findings demonstrate the interaction between physical-chemical variables, Chl-a, and zooplankton and highlight the significance of ecological understanding of the complex dynamics of the food web system in shallow tropical lakes such as Lake Malombe-under the changing climate.