Abstract: Water level fluctuations mediate species composition and abundance dynamics of zooplankton to impact the structure and function of aquatic ecosystems. There are many temporary pools formation along the bed of Ganjiang River due to water level decline in dry season. To explore the variation of zooplankton communities in pools and adjacent riffles, three pools and riffles, located in Nanchang section of Ganjiang River, were used to collect zooplankton in January and March of 2015 to investigate species composition, density, biomass, species diversity, and community structure. Water environment factors, zooplankton density and biomass in pools and riffles were analyzed by one-way ANOVA to test the variance. Zooplankton communities in pools and riffles were analyzed by Non-metric multi-dimensional scaling (NMDS) and analysis of similarity (ANOSIM) with software Primer 5.0. A total of 44 species of zooplankton were identified. Among them, 30 rotifers (68%), 7 cladocerans (16%) and 7 copepods (16%) were recorded. There were five dominant species with index of relative importance greater than 1000, which were Sinocalanus dorrii, Polyarthra dolichoptera, Copepod nauplii, Brachionus angularis and Synchaeta oblonga. The results of one-way ANOVA suggested that water depth, conductivity and total nitrogen of pools were significantly higher than those of riffles (P<0.05). In January, the water temperature, pH, dissolved oxygen, turbidity and total phosphorus of riffles were slightly higher than those of pools. In March, the water depth, pH and total nitrogen of pools were slightly higher than those of riffles. Dissolved oxygen, turbidity and total phosphorus of riffles were higher than pools. The water temperature and conductivity in the two water bodies were very close. In January, the total density (7.90 ind./L) and biomass (7.78 μg/L) of zooplankton in pools were lower than those in riffles (9.34 ind/L, 19.03 μg/L). On the contrary, the total density (24.27 ind./L) and biomass (332.14 μg/L) of zooplankton in pools were higher than those in riffles (22.86 ind./L, 146.10 μg/L). The Shannon-winner index (H'), Pielou evenness index (J) and species richness index (D) of zooplankton in riffles were higher than those in pools. Marginally significant difference in zooplankton communities between pools and riffles in January (P=0.067) were found by non-metric multi-dimensional scaling and similarity analysis. Zooplankton communities in January showed two communities: pool community and riffle community. In March, pools and riffles were gradually connected with the rising water level. There were no significant differences in zooplankton communities between the two habitats (P=0.313). Spearman correlation coefficient showed that water depth and dissolved oxygen were main environmental factors in variation of zooplankton density between pools and riffles. Zooplankton communities had significant correlations with pH, conductivity, total nitrogen and phosphorus (P<0.05) in the two habitats.