Relatively little is known about the factors that regulate in-water biogeochemical processes and food chains in prairie wetlands, or whether these systems are net sources or sinks of greenhouse gases such as carbon dioxide or methane. No published data are available to indicate which of these roles prairie wetlands play or how these roles may shift under different climatological conditions.

Arid conditions expected as a result of climatic warming may have an effect on the biogeochemistry of prairie wetlands. Drier conditions could cause changes not only in the ionic chemistry of these wetlands, but also in the chemistry, production and utilization of dissolved organic carbon or DOC. Any of these changes has the potential to significantly affect overall wetland carbon cycling. Under climatic change scenarios, DOC concentrations could increase because of the interacting effects of evapotranspiration and increased autochthonous DOC production. No studies have been made of the relative importance of autochthonous and allochthonous DOC sources in wetlands.

Increased aridity can also affect the salinity of a wetland, as wetlands are naturally saline and increased evaporation increases the salt concentration. This increase in salinity could have an effect on wetland DOC concentration and its molecular weight size distribution. Increases in the amount of low molecular weight DOC arising from increased salinity might negatively affect overall carbon cycling in these systems, but this likelihood remains speculative. Unfortunately, studies of overall carbon cycling, specifically microbial production and the factors that regulate it, are lacking for prairie wetlands.

In studies of long-term changes in prairie wetland chemistry, there appears to be no data on DOC. There is no information regarding external processes that may affect not only the rate of accrual of DOC to prairie wetlands, but also the quantity and quality of DOC. Climatic warming, increased UV-radiation, and agriculture activity all have the potential to have extreme effects on the biogeochemistry and food chains of prairie wetlands. It is therefore imperative to obtain an understanding of the major biogeochemical processes in prairie wetlands and how these may be affected by external perturbations related to atmospheric change and agriculture. Construction of a carbon model for a prairie wetland would be an important initial step in this process.