Riparian forests are assumed to play a crucial role in the global carbon cycle. However, little data are available on C stocks of floodplains in comparison to other terrestrial ecosystems. In this study, we quantified the C stocks of aboveground biomass and soils of riparian vegetation types at 76 sampling sites in the Donau‐Auen National Park in Austria. Based on our results and a remotely sensed vegetation map, we estimated total C stocks. Carbon stocks in soils (up to 354 t ha–1 within 1 m below surface) were huge compared to other terrestrial ecosystems. As expected, soils of different vegetation types showed different texture with a higher percentage of sandy soils at the softwood sites, while loamy soils prevailed at hardwood sites. Total C stocks of vegetation types were significantly different, but reflect differences in woody plant biomass rather than in soil C stocks. Mature hardwood and cottonwood forests proved to have significantly higher total C stocks (474 and 403 t ha–1, respectively) than young reforestations (217 t ha–1) and meadows (212 t ha–1). The C pools of softwood forests (356 t ha–1) ranged between those of hardwood/cottonwood forests and of reforestations/meadows. Our study proves the relevance of floodplains as possible C sinks, which should be increasingly taken into account for river management. Furthermore, we conclude that plant‐species distribution does not indicate the conditions of sedimentation and soil C sequestration over the time span of interest for the development of soil C stocks.