This category of habitat types includes brackish and freshwater marsh and associated high marsh. The majority of marsh at Cedar Island Refuge is brackish marsh with varying levels of salinity in the surface and groundwater. This habitat type is present on the refuge in large continuous blocks that are relatively intact and unaltered. Great marsh is a contiguous and unbroken expanse of 5,000 acres, and is a unique feature of the refuge.

Much of the natural brackish marshes have a natural fire frequency of one to three years, but have endured fire exclusion during the past half century or longer. As a result, many of them are suffering from a lack of species diversity as only one to three species of marsh grasses dominate the wetter or lower marshes, and encroaching brush has now dominated the high marshes. Large mats of wrack and storm debris have drifted up in long wide tide lines, suffocating large strips of marsh. Dead grass makes up a large component of the remaining marsh stands, limiting plant productivity and nutrient availability and adversely affecting wildlife habitat. Cedar Island Refuge has 11,000 acres of marsh habitat.