Coastal wetlands comprise important global carbon sinks; however, anthropogenic disturbance accompanied with accelerating sea-level rise threaten their continued survival. In this study, we quantified habitat disturbance to salt marshes in Barnegat Bay, New Jersey, resulting from the construction of ponds for mosquito control. Geographic object-based image analysis of high resolution four-band imagery revealed that over 7,000 ponds were constructed in the marsh complex with pond densities as high as 290 ponds per km2. Physical disturbance from pond creation and sediment dispersal extended to over 17% of the Bay’s tidal wetlands. By tracking recolonization of vegetation, we estimated it took 5 years for 51% vegetation recovery, 10 years for 69% recovery, with complete recover (100%) not expected for more than 50 years. This suggest that efforts to extend the lifespan of drowning coastal wetlands through sediment additions might disrupt carbon dioxide assimilation, as effects of disturbance persist. Focusing on greenhouse gas exchange, our work found that areas of marsh vegetation contribute to carbon assimilation (-42 g C m-2 y-1), while ponds and areas of bare peat created by pond excavation were associated with carbon emissions (44 and 125 g C m-2 y-1, respectively). These results suggest that the conversion of wetlands to ponds – which is a significant driver of coastal wetland loss worldwide – may convert coastal wetlands from greenhouse gas sinks to sources. Additionally, quantifying the area of vegetation within a marsh (vs. bare ground or open water) is important for quantifying their greenhouse mitigation function.