Microorganisms are recognized as sensors of extal disturbance in freshwater ecosystems. In this study, sediment samples from regions with strong human activity interference (four sites), moderate human activity interference (five sites) and minor human activity interference (five sites) in Baiyangdian Lake were collected; and their physiological and chemical properties and heavy metals contents were analyzed. The structures of bacterial and fungal communities were tested using 16S ribosomal Ribo-nucleic Acid (rRNA) and Intal Transcribed Spacer 2 (ITS2) high-throughput sequencing technologies. The results indicated that Proteobacteria was the most abundant bacterial phylum. Ascomycota, Basi-diomycota and Ciliophora were the dominant phyla of fungi. Obvious differences of microbial genera among the three regions were observed, especially fungal genera. With intensified disturbance by human activities, the Simpson and Shannon indices of bacteria significantly decreased. The fungal communities were clustered into three groups in accordance with the different human disturbance levels. The bac-terial communities of sediment samples under moderate and minor human disturbance appeared similar, but different from those under strong human disturbance. Redundancy analysis indicated that zinc, total phosphorus, copper, and lead were the dominant factors that influenced the bacterial com-munity. Nitrifiers and sulfate-reducing bacteria were influenced by pH, nitrate (NO3-), and total nitrogen. The fungal community was significantly affected by total phosphorus. This study reveals that sediment microbial community structures among different regions of a shallow lake are mainly impacted by human activities.