Small rivers provide important ecosystem services and harbour a rich biodiversity. Nevertheless, their ecology is still poorly understood in many parts of the world due to the paucity of studies. To this end, the water quality and zooplankton structure of several first order rivers in Ebonyi State, Nigeria were studied for the first time to assess the factors that influence the species diversity, abundance and biomass. Samples for water quality parameters and zooplankton analyses were collected for eighteen months using a standard procedure. The results showed a significant 

(p < 0.05) seasonal variation in mean air and water temperatures, conductivity, total dissolved solids, flow rate, and dissolved oxygen. Rotifera dominated zooplankton abundance and biomass and were the most diverse group. Cladocera contributed most to zooplankton species richness at the Ebyia and Idumayo rivers in the dry and rainy season, respectively. The dominance of Brachionus spp., Filinia longiseta, Cyclops spp. and nauplii indicated organic pollution at some of the rivers in the dry season. The Canonical Correspondence Analysis showed that temperature, water flow rate, transparency, conductivity, TDS, dissolved oxygen, and available phosphate were the major factors that affected zooplankton abundance, diversity, species richness and biomass in the rivers during the study.