We investigated benthic macroinvertebrate communities in three contrasting habitats of a large shallow lake from February to November 2009. The three habitats differed markedly in their environmental characteristics (e.g., trophic status, substrate type, wind exposure). A total of 36 species were collected from the three habitats. The calculated descriptors (abundance, biomass and Pielou evenness index) differed significantly among the habitats. Generally, Tubificidae, Bivalvia and Gastropoda dominated the benthic community in abundance and biomass, but they varied greatly in abundance among the habitats. Analysis of similarities (ANOSIM) and non-metric multidimensional scaling (NMDS) analyses revealed significantly different macroinvertebrate assemblages among the habitats. North Bays had the lowest biodiversity and were exclusively dominated by pollution-tolerant species (e.g., Limnodrilus hoffmeisteri and Rhyacodrilus sinicus). Communities in the open lake contained intermediate biodiversity and were characterized by five species belonging to several taxonomic groups (e.g., Corbicula fluminea, L. hoffmeisteri and Gammarus sp.). Macrophyte-dominated habitats (East Bays) presented the highest diversity and evenness and were mainly characterized by gastropods. A canonical correspondence analysis (CCA) demonstrated that habitat-specific differences in trophic status, pollution level, wind-induced disturbance and macrophyte distributions were highly correlated with macroinvertebrate community structure.