Global acknowledgement of climate change and its predicted environmental consequences has created a need for practical management techniques that increase a landscape’s ability to capture and store atmospheric carbon (C). Globally, wetlands sequester disproportionally more C per unit surface area than many other components of the landscape. However, wetlands vary in their capacity to store C and regulate greenhouse gas emissions. Hydrology, in particular, is a critical driver of wetland C capture and storage. Rain-filled wetlands offer a challenge for the management of C sequestration and storage because the hydrology of these systems is almost entirely driven by rainfall. We present a conceptual model of how management options, including weed and pest control, grazing and crop management and revegetation, will affect C sequestration and storage in rain-filled wetlands. Given the intensive nature of agricultural activities in areas where rain-filled wetlands are common, further work is needed to increase our understanding of the effects of these activities on wetland C capture and storage. Key knowledge gaps relating to the effect of management actions on wetland C sequestration include: (a) the benefits of integrated wetland management; (b) the appropriateness of different grazing regimes and the effect of total grazing pressure; (c) the effects of fire; and (d) the extent to which wetland function (C storage) can be restored following agricultural activities, such as cropping.