In this work, BIOLOG community-level physiological profile (CLPP) technique was employed to explore the bacterial community functional diversity from different depth (0.5 m, 30 m and 65 m) and sites (site A, site B and site C) of the JIN PEN drinking reservoir, China. The results showed that the highest bacterial community activities expressed as average well color development (AWCD_590nm) was observed in 30 m, the lowest was observed in 65 m. The significant “sites” and “depth” indicates that the AWCD_590nm varied among the sites within the depth (P<0.01). Whilst, species richness diversity (R) was significantly higher in 30 m than that of 0.5 m and 60 m, but there were no significant two-way interactions for R and Shannon’s diversity index (P>0.05). Meanwhile, Principle component analyses (PCA) of BIOLOG profiles indicated that bacterial community functional diversity was changed in different depths and sites. Carbon substrates with highest significant correlation coefficients for PC1 and PC2 were hydroxy butyric acid and mannitol. Overall the findings increased our knowledge about the aquatic bacterial community diversity in drinking water constitute a potential health risk, because increased functional microbial communities may influence drinking water quality.