The structural composition of zooplankton of two lakes (Ossa and Mwembe) of the Ossa complex, a UNESCO’ protected site located in Dizangue, Cameroon, was studied. Monthly sampling was conducted from September 2009 to February 2010. The physicochemical characteristics of the water lakes, the characteristics of the area around the lakes were documented and their influence on zooplankton communities assessed. The two lakes were closes in accord to their physicochemical characteristics: temperature (27.70±0.87°C and 28.85±0.66°C), pH (6.57±0.06 and 6.52±0.07), Suspended Solids (7.00±2.39mg.L-1 and 10.66±3.12mg.L-1), electric conductivity (28.91±5.25µS.cm-1 and 28.18±7.33µS.cm-1). In fact, no significant difference was found, compare to each other. Thirty seven and 41 species of zooplankton were recorded in the Ossa and Mwembe lakes respectively. The seasonal variation appeared to be the fundamental factor that regulates the presence and abundance of these species in the lakes. Lecane sp., Polyarthra vulgaris, Epiphanes clavulata, Lepadella sp., Brachionus dimidiatus and Plationus patulus were mostly abundant during the dry season whereas Bosminopsis macaguensis, Bosminopsis deitersi, Keratella tecta, Hexarthra mira and Lecane bulla were abundant during the rainy season. When taking into consideration the contents of phosphorus and Secchi disc disappearance, these lakes were found to be eutrophic. In addition, the Sanaga River brings sporadic zooplankton species such as Scaphaloberis kingi and Streblocerus sp., contributing to the accumulation of crustacean eggs on the river banks during floods, and therefore to increase the density of organisms. In conclusion, the effluents from SAFACAM Company increase some physicochemical parameters values such as, electric conductivity, dissolved carbon dioxide and pH.