Methods based on functional traits are widely used in current biodiversity studies. As an important component of aquatic food web, the attention paid on zooplankton by researchers is disproportional to its functional importance. In the present study, the effects of environmental factors on functional diversity indices as well as on distribution of functional groups of crustacean zooplankton communities in 14 waterbodies were investigated. The results showed that species with similar functional traits were grouped together and phylogenetically related. Correlation analysis found no significant correlation between functional richness (FRic), functional evenness (FEve), functional divergence (FDiv) and environmental factors. However, significant relationships were found for functional dispersion (FDis) in relation to total dissolved nitrogen, total dissolved phosphorus(TDP), ammonia nitrogen and seston C/P ratio. Regression analysis found that except species richness, number and Shannon-Wiener index of functional groups as well as FDis all declined significantly with the increasing concentration of TDP. In addition, FRic and FDis were both positively correlated with the number of functional groups. These results suggest that eutrophication induces the clustering of functional traits of crustacean zooplankton, and environmental filtering is one of the major forces in driving the formation of crustacean zooplankton community structure.