Wetlands exhibit high primary productivity and play a significant role in the global carbon cycle. Brackish and salt marshes co-occur in Southern California; yet, restoration designs often eliminate remnant brackish marshes, along with their ecosystem functions, without evaluation. Vegetation, soil organic matter, and carbon flux were compared between brackish and salt marsh habitats in the Huntington Beach Wetlands. Newland Brackish Marsh had more carbon aboveground in denser and taller vegetation than the other two marshes. Brookhurst Salt Marsh sediments had more organic matter than the other two marshes. CH₄ emissions were negligible at all sites, and there were no differences in CO₂ flux or aerobic and anaerobic microbial respiration among sites. Although these components of the carbon cycle were similar among sites in this project, such quantitative functional evaluations should be part of the restoration planning process.