Inland waters process large amounts of organic carbon, contributing to CO2 and CH4 emissions, as well as storing organic carbon (OC) over geological timescales. Recently, it has been shown that the magnitude of these processes is of global significance. It is therefore important to understand what regulates OC cycling in inland waters and how is that affected by climate change. This thesis investigates the constraints on microbial processing of sediment OC, as a key factor of the carbon cycling in boreal lakes. Sediment bacterial metabolism was primarily controlled by temperature but also regulated by OC quality/origin. Temperature sensitivity of sediment OC mineralization was similar in contrasting lakes and over long-term. Allochthonous OC had a strong constraining effect on sediment bacterial metabolism and biomass, with increasingly allochthonous sediments supporting decreasing bacterial metabolism and biomass. The bacterial biomass followed the same pattern as bacterial activity and was largely regulated by similar factors. The rapid turnover of bacterial biomass as well as the positive correlation between sediment mineralization and bacterial biomass suggest a limited effect of bacterial grazing. Regardless of the OC source, the sediment microbial community was more similar within season than within lakes. A comparison of data from numerous soils as well as sediments on the temperature response of OC mineralization showed higher temperature sensitivity of the sediment mineralization. Furthermore, the low rates of areal OC mineralization in sediments compared to soils suggest that lakes sediments are hotspots of OC sequestration. Increased sediment mineralization due to increase in temperature in epilimnetic sediments can significantly reduce OC burial in boreal lakes. An increase of temperature, as predicted for Northern latitudes, under different climate warming scenarios by the end of the twenty-first century, resulted in 4–27% decrease in lake sediment OC burial for the entire boreal zone.