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.

The literature on ecological effects of recent climate change in fresh waters has been reviewed, with particular reference to freshwater conservation in the UK. Least emphasis is given to predictive models of future change, because of considerable uncertainties even in the climate models, let alone their biological implications. Climate change effects on fresh waters have been superimposed on existing large human impacts, which make separation of climatic effects particularly difficult.

Research in fresh waters has concentrated on communities and processes and there is less emphasis on individual charismatic species than in terrestrial systems. This approach lends itself to space-for-time studies on climate effects. There has been a modest amount of experimentation, particularly in mesocosms, and analysis of long-term biological data sets, the most extensive from lakes. The most detailed information on ecological effects comes from lake plankton.

No species is yet known to have been lost from the UK as a result of climate change but there is extensive evidence of changes in phenology and distribution, and in processes in the plankton. It is likely that temperature effects per se will be less important than effects of changed hydrology and that idiosyncratic behaviour of each species will lead to many indirect effects through biological interactions in communities. Experimental studies suggest major likely changes in plant, fish and invertebrate communities with a several degree increase in temperature and associated hydrological changes expected in the 21st century. Freshwater organisms, however, are well adapted to disturbance and through invasion, redistribution, adaptation and microevolution will re-form functioning communities, though with likely different biodiversity than at present. Some invasive species may come to dominate the new communities. There will be important consequences for the estimation of ecological quality, which will inconvenience statutory obligations under the Water Framework Directive, and symptoms of eutrophication will be exacerbated. Some coastal lakes may revert to estuaries.

Much more important, however, may be the consequences of climate change for the important part of the carbon cycle that is focussed on fresh waters, particularly if the ratio of community respiration to gross primary production increases with rising temperature. Several studies suggest large increases in this ratio with temperature rises of up to 4 °C. A much more radical approach to conservation, involving re-establishment of entire, connected catchment systems rather than the present piecemeal attention to biodiversity issues is likely to be needed if a comfortable human future is to be guaranteed.