Sampling was carried out in wet season and dry season of 2012 in order to analyze the distribution of chlorophyll-a and the effects of water environment factors on chlorophyll-a in Dongjiang River, Pearl River basin. Results showed chlorophyll-a concentration appeared strong temporal and spatial variations in Dongjiang River, ranging from 0.84 to 14.93μg/L, and with the annual mean value of 3.60±2.45μg/L. The chlorophyll-a concentration in wet season was obviously higher than that in dry season. For wet and dry season, the temporal distribution of chlorophyll-a had a similar pattern, increasing from upstream to downstream. The correlation analysis and principal components analysis indicated TN, TP, COD_Mn, water temperature and flow velocity were the most important factors for the growth of phytoplankton in Dongjiang River, and phosphorous might be the limiting factor because of its remarkable influence on phytoplankton.