Lake sediments are important areas for remineralisation of nutrients involved in phytoplankton blooms. This study simultaneously analysed the microbial community structure and measured the sediment fluxes of inorganic nitrogen, phosphorus and silica from sediment cores collected at 2 different locations within a sub-tropical polymictic reservoir, Lake Wivenhoe. The bacterial and archaeal community structure was determined by amplifying and cloning the 16S rRNA gene from co-extracted DNA and RNA samples. A total of 19 phyla or candidate divisions of bacteria were identified, with sulphur-reducing bacteria within the phylum of Deltaproteobacteria being the most abundant ribotypes in DNA-derived clones libraries. In contrast, Actinobacteria and Acidobacteria were the most abundant ribotypes in RNA-derived clone libraries from the upper and lower sediments, respectively. The archaeal community was dominated by Euryarchaeota, with methanogenic archaea belonging to subdivisions of Methanobacteria and Methanomicrobia accounting for 69 to 98% of the sequenced clones. Comparison of the 16S rDNA and rRNA clone libraries revealed that bacterial groups highly abundant in the sediments were mostly metabolically inactive, whilst those metabolically active were not very abundant. A higher relative abundance of nitrifying ribotypes (Nitrospira sp.) was identified at Site B, which corresponded to a higher efflux of nitrate from the sediments to the water column at this site. At the time of sampling, Lake Wivenhoe was stratified, and sediment cores were collected from the hypolimnion. Our results suggest that water column depth and delivery of dissolved oxygen to the sediments influenced the sediment microbial community structure and the fluxes and speciation of nutrients, which are reported to influence phytoplankton species composition and bloom dynamics.