Sediment cores taken from Great SlaveLake, Canada, were analysed to investigate theirmetabolically active microbial populations and geochemistry. The amplification of cDNA detectedmetabolically active bacterial (50 separate bands)and archaeal (49 separate band) communities. The bacterial communities were further resolved indicating active actinobacterial and c-proteobacterial communities(36 and 43 individual bands respectively).Redundancy discriminate analysis and Monte Carlopermutation testing demonstrated the significantimpact of geochemical parameters on microbial community structures. Geochemical analyses suggest that the upper 0.4 m represents soil weathering and erosion in the lake catchment. An increase in organic carbon in the lower core suggests either more primary productivity, indicating warmer climate conditions, associated with Holocene Climatic Optimum conditions pre 5,000 years BP or change from a reducing environment in the lower core to an oxidizing environment during more recent deposition. Drivers for bacterial, archaeal and actinobacterial community structures were sediment particle size, and its mineral composition. Depth also significantly affected cproteobacterial community structure. In contrast the organic carbon content did not significantly shape the microbial community structures within the sediment. This study indicates that geochemical parameters significantly contribute to microbial community structure in these sediments.