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Water salinization in semi-arid and arid regions is threatening freshwater or oligosaline ecosystems. Anthropogenic processes enrich nutrients of aquatic systems causing significant environmental effects. Bosten Lake in Xinjiang Province, China is an interesting ecosystem featuring a salinity gradient from fresh to subsaline, as well as a nutrition gradient from oligotrophic to mesotrophic. In the present study, we focused on the effects of salinity and nutrients in Bosten Lake by investigating the zooplankton assemblages and environmental factors from different sampling times. A total of 74 zooplankton taxa were found, consisting of 34 rotifers, 26 protists, 10 cladocerans, and 4 copepods. Although no significant differences were found among different sampling sites, zooplankton species richness, diversity, and evenness showed significant differences between sampling times, with August samples showing highest values along with water temperature and total nitrogen. Principal component analysis and representational difference analysis results showed that zooplankton abundance is correlated with water temperature and nitrogen, but showed no significant relationship with water mineralization or conductivity. The subsaline-tolerating zooplankton species in Bosten Lake made their community insensitive to salinity. The decrease of total nitrogen concentration in Bosten Lake probably implied a primary productivity increase, which subsequently caused the zooplankton diversity to increase in August.