Coastal wetlands store carbon dioxide (CO₂) and emit CO₂ and methane (CH₄) making them an important part of greenhouse gas (GHG) inventorying. In the contiguous United States (CONUS), a coastal wetland inventory was recently calculated by combining maps of wetland type and change with soil, biomass, and CH₄ flux data from a literature review. We assess uncertainty in this developing carbon monitoring system to quantify confidence in the inventory process itself and to prioritize future research. We provide a value-added analysis by defining types and scales of uncertainty for assumptions, burial and emissions datasets, and wetland maps, simulating 10 000 iterations of a simplified version of the inventory, and performing a sensitivity analysis. Coastal wetlands were likely a source of net-CO₂-equivalent (CO₂e) emissions from 2006–2011. Although stable estuarine wetlands were likely a CO₂e sink, this effect was counteracted by catastrophic soil losses in the Gulf Coast, and CH₄ emissions from tidal freshwater wetlands. The direction and magnitude of total CONUS CO₂e flux were most sensitive to uncertainty in emissions and burial data, and assumptions about how to calculate the inventory. Critical data uncertainties included CH₄ emissions for stable freshwater wetlands and carbon burial rates for all coastal wetlands. Critical assumptions included the average depth of soil affected by erosion events, the method used to convert CH₄ fluxes to CO₂e, and the fraction of carbon lost to the atmosphere following an erosion event. The inventory was relatively insensitive to mapping uncertainties. Future versions could be improved by collecting additional data, especially the depth affected by loss events, and by better mapping salinity and inundation gradients relevant to key GHG fluxes.