For climate mitigation it is important to identify and protect landscape units that have disproportionally large carbon storage (CS). Here we report on CS of the upper 30 and 60 cm of soil in transects of vegetation types in stream valleys in the Brazilian Cerrado savanna, including Pasture, nearly native Cerrado vegetation, Vereda wetlands, and Gallery Forests. We chose three areas with varying types of human impacts in each of which three degraded and reference transects were compared. For the 60 cm CS in undisturbed sites, maximum and average values per area were highest for Gallery Forest (360.0 and 206.5 Mg C ha−1) and Vereda wetland (201.9 and 142.4 Mg C ha−1), while those of Cerrado (57.7 and 52.7) and Pasture (62.3 and 52.7 Mg C ha−1) were considerably lower. Variation between the three areas was high. In an area degraded by cattle trampling, losses in the upper 60 cm compared to reference sites were highest in the carbon-rich vegetation types Vereda (72%) and Gallery Forest (71%) and lower in the carbon-poorer Pasture (33%) and Cerrado (7%). In areas degraded by fire or by erosion, results were less conclusive. Our data appeal to an improved conservation of riparian ecosystems of the Cerrado biome.