Bacterial communities in two shallow eutrophic aquatic ecosystems (eastern China) were studied using culture-dependent methods, and their correlations with the other water parameters were analyzed. Although the values of the comprehensive trophic state index in Xizi Lake and Hangzhou Canal were almost identical, the abundances of cultivable bacterial communities, such as protein-hydrolyzing bacteria (PHB), fecal coliforms (FC), nitrogen-utilizing bacteria, phosphate-mineralizing bacteria, and cellulose-decomposing bacteria (CDB), differed significantly. They were much less in Xizi Lake than in Hangzhou Canal. Correlation analyses indicated that the abundances of physiological groups of bacteria were determined mainly by the biomasses of phytoplankton and zooplankton, rather than by the utilized substrates. Xizi Lake was an algae-dominated aquatic ecosystem, a situation that mainly arose from the influx of inorganic nutrients, and the Hangzhou Canal was bacteria-dominated due to the influx of organic sewage. Molecular characterization and phylogenetic analysis of isolates showed that there were 6 phylogenetic lineages out of 15 isolates screened from Xizi Lake, including c-proteobacteria (5), b-proteobacteria (3), a-proteobacteria (2), actinobacteria (1), firmicutes (4), and bacteroidetes (1). While in Hangzhou Canal there were only 4 bacterial groups among 22 isolates, c-proteobacteria comprised about 82%, a-proteobacteria made up 9%, firmicutes and bacteroidetes made up only 4.5%, respectively, and no b-proteobacteria were found. Enterobacteriaceae were the principal bacteria components in the two aquatic ecosystems, especially in the sewage-polluted Hangzhou Canal. It can be concluded preliminarily that the bacterial diversity in Xizi Lake is richer than that in Hangzhou Canal.