In order to assess the zooplankton community in an anthropogenic-disturbance Badagry creek, Zooplankton and water samples were collected and analyzed bi-monthly from November 2011 to September 2013 in nine stations representing its three different zones using standard methods. Zooplankton was identified to species-level using relevant texts and counted under a Microstar IV Carl Zeiss binocular microscope calibrated at different magnifications. Diversity was determined using Shannon-Weiner (H), Simpson (1-D) and Evenness (e^H/S) indices. Water samples were analysed for temperature, pH, salinity, conductivity, turbidity, dissolved oxygen, water depth and nitrate. Data were analysed using descriptive statistics, ANOVA, cluster and Canonical correspondence analysis (CCA) at α = 0.05. A total of 56 species comprising 26 species of rotifers, 15 species of arthropoda, 4 species of ciliophora, 3 species of cnidaria, and 2 species of ctenophora, foraminifera, mollusca, protozoa each, with an array of meroplankton / juvenile stages of the order copepod of subphylum crustacea were recorded. Diversity indices were highest (H = 2.20; 1-D = 0.80; e^H/S = 0.27) at station 6 and lowest in station 8 (H = 1.20; 1-D = 0.56) and station 1(e^H/S = 0.14). Salinity/conductivity, nitrate and water depth were significantly different (p < 0.05) among the study stations. CCA revealed salinity/conductivity and nitrate were the most important abiotic factors co-related with the zooplankton abundance in Badagry creek. The moderately low zooplankton communities’ diversity and abundance in Badagry creek point at different natural and anthropogenic factor impacts.