Floodplains are important ecosystems that contribute to the ecological stability of the landscape. A number of ecosystem functions and services are significantly influenced by ecological aspects of floodplain habitats. This article focuses on the ecological quality and estimated amount of carbon stored in the biomass of habitats located in the studied watersheds, with an emphasis on floodplains. The habitats and their ecological quality were determined and assessed using the Biotope Valuation Method (BVM), an expert method for evaluating habitat (biotope) types based on eight ecological characteristics, mainly concerning various aspects of their biodiversity and vulnerability. The objective of this study is to compare the resulting assessments of habitats located in floodplains with assessments of habitats situated in the surrounding landscape. The study was carried out on three selected small stream watersheds in the South Moravian Region of the Czech Republic, which differ from each other in terms of the predominant land use and the overall level of anthropogenic pressure on the landscape. The results indicate that floodplains have a higher ecological value compared to the surrounding landscape, except for floodplains in areas with intensive agriculture. The ability of floodplains to store carbon in biomass turned out to be higher in the watershed with a higher percentage of tree stands, where woody plants store significantly more carbon in the biomass compared to other types of vegetation. It has been shown that human pressure on floodplains and land use significantly affects ecosystem functions and services. In addition to the intensity of agriculture, these were, in particular, pressures from an expansion of built-up areas and infrastructure developments, and forest management. In this study, forest stands in floodplain were more stable and had a more beneficial species composition than forests in the surrounding landscape.