Wetland carbon budgets largely depend on the wetland communities’ relative rate of carbon assimilation and carbon emission. Invasive plants with growth or decomposition patterns that differ from reference plant communities may shift wetland carbon budgets, as may invasive plant suppression efforts. For example, Phragmites australis (European Common Reed), which replaces meadow and cattail marsh in the Laurentian Great Lakes area, has high biomass production and foliar nitrogen, can modify the environment conditions that effect decomposition rates, creates thick stands of slowly decomposing standing dead stems, and is often controlled using broad-spectrum herbicides. Our objectives were to determine if P. australis control efforts in freshwater coastal marshes were sufficient to return net primary productivity, decomposition rates, and environmental conditions to within their pre-invasion range. We find that P. australis invasion had the greatest effect on carbon sequestration when replacing meadow marsh, as opposed to cattail marsh. We conclude that control efforts, one-year post-treatment, dramatically reduce total biomass and carbon assimilation compared to meadow and cattail marsh. However, floating and submersed aquatic vegetation rapidly colonized treated areas, suggesting that continuing plant community recovery may restore the carbon budget in subsequent years.