Lakes play a major role in the global carbon (C) cycle, despite making up a small area of earth’s surface. Lakes receive, transport and process sizable amounts of C, emitting a substantial amount of the greenhouse gases, carbon dioxide (CO2) and methane (CH4), into the atmosphere. Ice-covered lakes are particularly sensitive to climate change, as future reductions to the duration of lake ice cover will have profound effects on the biogeochemical cycling of C in lakes. It is still largely unknown how reduced ice cover duration will affect CO2 and CH4 emissions from ice-covered lakes. Thus, the primary aim of this thesis was to fill this knowledge gap by monitoring the spatial and temporal dynamics of CO2 and CH4 in ice-covered lakes. The results of this thesis demonstrate that below ice CO2 and CH4 were spatially and temporally variable. Nutrients were strongly linked to below ice CO2 and CH4 oxidation variations across lakes. In addition, below ice CO2 was generally highest in small shallow lakes, and in bottom waters. Whilst below ice CH4 was elevated in surface waters near where bubbles from anoxic lake sediment were trapped. During the ice-cover period, CO2 accumulation below ice was not linear, and at ice-melt incomplete mixing of lake waters resulted in a continued CO2 storage in bottom waters. Further, CO2 transported from the catchment and bottom waters contributed to high CO2 emissions. The collective findings of this thesis indicate that CO2 and CH4 emissions from ice-covered lakes will likely increase in the future. The strong relationship between nutrients and C processes below ice, imply that future changes to nutrient fluxes within lakes will influence the biogeochemical cycling of C in lakes. Since catchment and lake sediment C fluxes play a considerable role in below ice CO2 and CH4 dynamics, changes to hydrology and thermal stability of lakes will undoubtedly alter CO2 and CH4 emissions. Nevertheless, ice-covered lakes constitute a significant component of the global C cycle, and as such, should be carefully monitored and accounted for when addressing the impacts of global climate change.