Abstract: Xiashan Reservoir, the premier reservoir in Shandong Province, serves as a crucial source of drinking water. However, escalating human activities and environmental pressures have posed formidable challenges to its ecological equilibrium. A notable gap in research regarding the microbial composition of its water body and sediments, which hold significant ecological and economic importance, has hindered our comprehension of its ecosystem functions and the development of effective conservation measures. To address this, we conducted a comprehensive analysis of microbial composition in June 2023 using high-throughput sequencing of bacterial 16S rRNA genes. Our findings revealed that the microbial diversity indices, including Sobs, Chao1, Ace, and diversity, were significantly higher in the sediments compared to the water body, underscoring the richer and more diverse microbial communities in the sediments. β-diversity analysis further emphasized distinct microbial compositions between these two environments. In the water body, Actinobacteria (57.65%), Proteobacteria (34.9%), and Bacteroidetes (6.22%) were the dominant bacterial phyla, with the most abundant genera being hgcI_clade (29.98%), Limnohabitans (17.06%), CL500-29_marine_group (11.97%), and Sporichthyaceae (7.12%). Conversely, the sediments were predominantly inhabited by Proteobacteria (39.63%), Bacteroidota (12.70%), Desulfobacterota (9.88%), Chloroflexi (6.79%), Nitrospirota (5.56%), and Acidobacteriota (3.52%), with Steroidobacteraceae (6.98%), Thermodesulfovibrionia (4.97%), Thiobacillus (4.33%), Sutterellaceae (4.07%), and SC-I-84 (3.48%) as the leading genera. Although the dominant bacterial groups in Xiashan Reservoir exhibit similarities to those found in other domestic reservoirs, the presence of potential fish pathogens such as Flavobacterium and Aeromonas underscores the risk of fish diseases. Functional prediction analysis indicated that microbial functions in both water and sediments were largely congruent, with metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, biosynthesis of amino acids, and carbon metabolism being the most prominent metabolic pathways at level 3 prediction. Notably, immune diseases-related functions were significantly more abundant in the water body compared to the sediments. This study provides valuable insights into the ecological functions of the reservoir and offers essential background information for evaluating the effectiveness of future ecological management efforts.