Sediments microbial communities in aquatic environments are important because they are fundamental to biogeochemical and energy cycling, productivity as well as "buffering" capacity of aquatic ecosystems. We collected sediment samples from four stations characterized by different aquatic environmental conditions during two periods of times and investigated effects of nutrient factors on sedimentary microbial biomass and community structures using phospholipid fatty acid (PLFA) analysis. All four sampling stations were located around Luma Lake, a moderately eutrophic reservoir located in Jiangsu province, China. The result suggested that the sedimentary microbial biomass at all four sampling stations displayed a negative relationship to water temperatures and a positive relationship to degrees of eutrophication. Spatial scales of heterogeneity in sedimentary microbial biomass were affected by environments factors, i.e. they were more sensitive in eutrophic area. Spatial patterns and variation over time in sedimentary microbial community structure of Suqian water gate and Malingfan stations, which were characterized by similar riverine hydrological conditions and being moderately polluted, were alike. Principal component analysis suggested that it was more easily for microeukaryotes to be affected by aquatic environmental factors. Utilizing RDA, we found that total phosphorous, total nitrogen and ammonium-nitrogen were strongly associated with microeukaryotes and gram-positive bacteria positively, yet the ratios of microeukaryotes to bacteria and the ratios of gram-negative bacteria to gram-positive bacteria, which were considered to be community structure indicators, had no identifiable relationships with any nutrient factor.