Wetlands are widely recognized for their carbon (C) sequestration capacity and importance at mitigating climate change. Yet, to best inform regional conservation planning, the variability of C stocks among wetland types and between above and belowground compartments requires further investigation. Additionally, the bathymetry of peat basins has often been ignored, with soil C stock calculations mostly relying on the thickest peat section, potentially leading to overestimates. Here, we sampled vegetation and soil of 57 wetlands of southeastern Canada to characterize the variability of above and belowground organic C stocks among four wetland types: open bogs, open fens, swamps, and forested peatlands. We also compared carbon stock estimation approaches considering peat bathymetry or not. Results showed that peat thickness, and thus soil organic C (SOC), varied substantially within sites due to peat basin shapes. Omitting bathymetry led to site-scale SOC overestimates of about 20–38 % on average, depending on the approach used, with wide variability among sites (overestimates up to 200 %). Belowground C stocks varied among wetland types with mean values of 132, 101, 19, and 44 kg C m−2 for bogs, fens, swamps, and forested peatlands, respectively. Aboveground C was nearly zero in open bogs and fens but reached ∼30 % of total C stock in swamps and ∼ 15 % in forested peatlands. C stocks in tree roots and shrubs were negligible. Despite the lower C density (per m2) of swamps and forested peatlands, these ecosystems represented the dominant C stocks at the regional scale due to their abundance in the landscape. Overall, the four wetland types stored an estimated 2–7 times more C than forest per unit area. Evaluating differences in C stocks according to wetland type, while integrating peat bathymetry in calculations, can significantly improve regional wetland conservation planning.