Wetlands play a very important role in ecosystems. Qixinghe Wetland is a nature reserve area in northeastern China. In this paper, diatom communities and environmental qualities were investigated at eight sites in Qixinghe Wetland. This study was to examine diatom species patterns in relation to environmental variables in wetlands, and to use diatoms as indicators to water quality in wetlands and wetland classification. Diatoms were sampled in summers and autumns in 2002 and 2004, during which 180 taxa were identified. Environmental variations in pH, temperature, biochemical oxygen demand (BOD), and chemical oxygen demand (COD) were measured. The seasonal composition and abundance of diatoms changed greatly during the study period. The relationship between diatoms and chemical water quality was estimated statistically. Canonical correspondence analysis (CCA) with forward selection and Monte Carlo permutation tests revealed that all water environmental variables changed during the study period (P<0.05). Among all the parameters, variation in BOD among the sites was a very important determinant of species composition according to the CCA, and BOD decreased from 2002 to 2004. Our results suggest that the water quality had improved during the three-year period because of enhanced environmental protection with less human disturbance. We conclude that diatoms can be used to indicate water quality and habitat conditions in this wetland.