AbstractGlobally, there is little information on freshwater (non‐tidal) wetland below ground soil organic carbon (SOC) stocks, sequestration rates and, in particular, their within‐wetland variation. This basic information is critical for designing programs to sample SOC stocks and identifying areas that sequester large amounts of carbon so that they can be managed to prevent degradation and carbon loss. Here, focusing on temperate seasonally inundated freshwater wetlands in south‐eastern Australia, we compared SOC stocks and sequestration rates (via radiometric dating) among wetlands, within wetland locations (High water mark, Edge and Middle), and with adjacent terrestrial locations. SOC stocks varied most among wetlands but also varied inconsistently within wetlands. Wetland SOC stocks (20.4 ± 0.1 kg C m−2) were significantly greater than adjacent terrestrial locations (13.3 ± 0.1 kg C m−2). Wetland SOC sequestration rates were similar among all locations (i.e., within a wetland, ranging from 70 g C m−2 yr−1 to 87 g C m−2 yr−1). The relative lack of difference in SOC stocks among wetland locations allows for reduced within‐wetland sampling and subsequently greater replication at the wetland level, at least for temperate ephemeral freshwater wetlands, although these findings need to be confirmed over a range of wetland types. This study also produced the first estimates of temperate freshwater wetland SOC stocks and sequestration rates in Australia, and is among the first studies globally to demonstrate that seasonally inundated wetlands can sequester carbon at significant rates. It therefore provides important justification to support the protection and rehabilitation of temperate freshwater wetlands worldwide.