The study was conducted in the Qua Iboe River system between January 2020 and June 2021 in five sampling locations to investigate zooplankton composition and its relation with environmental variables. Water samples were collected using sterilised plastic bottles, while samples for biochemical oxygen demand were collected using 250 mL reagent bottles and analysed following the standard examination methods. Water temperature, hydrogen ion (pH), dissolved oxygen (DO), electrical conductivity (EC) and total dissolved solids (TDS) were measured in situ while water samples were collected for determination of sulphate (SO4-), nitrate (NO3-), ammonia (NH3), biochemical oxygen demand (BOD5), chemical oxygen demand (COD), chloride (Cl-), total suspended solids (TSS), total alkalinity (TA) and phosphate (PO4) in the laboratory. Zooplankton samples were collected by towing 55µm mesh size of plankton net for ten minutes. The concentrated zooplankton samples on the towing net were filtered into one-litre sampling bottles and preserved with two drops of 4% formalin solution, and identified using standard keys. The results showed that mean values for pH, DO, BOD5, COD, TSSand PO4 in some locations, deviated from the permissible limits. The zooplankton recorded was dominated by Rotifera (38.93 %), while Protozoa (9.2 %) was the lowest. The maximum species (905, 27.42 %) were obtained in location 1, while the minimum (550, 16.66 %) was in location 5. The study revealed that all the investigated water parameters except temperature, TSS and COD were negatively influenced the abundance of zooplankton owing to anthropogenic activities. Thus, the river should be protected by regulating the level of economic activities within the watershed, in order to improve water quality, maintaining the ecological integrity, and the socio-economic services they provide.