Carbon cycling is a cornerstone concept of ecosystem ecology, which has implications for climate change, ecosystem health, and human activities. This review investigates pathways of carbon within freshwater ecosystems, the role of terrestrial carbon in food webs, and the effects of food web structure on C emissions. Carbon may co-limit primary production even in waters super-saturated with CO₂. Allochthonous carbon-subsidies make most lakes and rivers net heterotrophic; however, the use of carbon-subsidies by the food web (FW) may be limited by low nutritional quality of terrestrial C-compounds and the inability of bacteria to synthesise polyunsaturated fatty acids (PUFA), which are essential for metazoan growth. Bacterivorous nanoflagellates which can synthesise PUFA are likely to create a channel connecting allochthonous C with metazoan production in some water bodies. Published studies suggest that FW structure may affect: carbon fluxes in and out of lake ecosystems; carbon accumulation and distribution within food webs; burial of carbon and carbon sequestration. Food web structure and nutrients can affect the carbon-emission/sequestration ratio and shift the state of the aquatic ecosystem between being a source or a sink for atmospheric carbon. Small lakes, such as farm ponds, are the dominant type of world fresh waters with highest carbon burial rates. Their productivity and FW structure are often modified by humans through nutrient fertilisation and fisheries management. We hypothesise that the planned management of these activities targeting a desirable emission/sequestration ratio, can be used as a tool for the reduction of carbon emissions to the atmosphere.