Soil microbial activity and community diversity in water level fluctuation zone (WLFZ) of the drinking water reservoir is still not well understood. In this context, soil dehydrogenase activity and bacterial community diversity of a drinking water reservoir was determined aiming to examine the water level fluctuation driving soil bacterial community activity and diversity across both vertical and longitudinal transects. BIOLOG method was employed to explore functional diversity of WLFZ soil bacterial community. The results shown that the highest dehydrogenase activity, 2.64 ìg TF/g.24h, was found in the top of WLFZ, which was 2.67 times higher than that of the bottom. Meanwhile, the average well color development (AWCD) _590nm, species richness and Shannon’s diversity of bacterial community associated with top of WLFZ was also significant higher than that of the bottom. The significant “site” and “WLFZ” revealed that the dehydrogenase activity, AWCD_590nm and species richness varied among the sites within the WLFZ (P<0.01). However, there were no significant two-way interactions for different sites (P>0.05). Heatmap and principle component analyses (PCA) of bacterial community metabolic fingerprints suggested a significant discrimination soil bacterial community in the bottom, middle and top of three different sampling sites of WLFZ. The higher  discriminate  carbon  substrates utilization by WLFZ soil bacterial community were cellobiose, hydroxy benzoic acid, tween 80, arginine, threonine, pyruvic acid methyl ester, ketobutyric acid, malic acid, glucosaminic acid and glycogen. These founding demonstrated that water level draw down affect soil microbial activity and bacterial community functional diversity in the water level fluctuation zone of the JIN PEN drinking water reservoir.