Climate-driven hydrological changes are transforming river valleys, particularly floodplain lakes (FLs). Increasingly prolonged droughts and reduced flooding are causing the desiccation of oxbow and floodplain lakes, leading to the conversion of aquatic sediments into soils. This study investigates both the quantity and quality of carbon in these environments by analysing submerged sediments and sediments transformed into soils in small FLs of the Middle Vistula Valley (central Poland). Samples from eight FLs, representing both submerged and desiccated zones, were analysed for total organic carbon (TOC), humic substances (HSs), fulvic acids (FAs), humic acids (HAs), and carbonates (CaCO3). The TOC content averaged about 40 g kg−1 in both sediments and soils, indicating considerable carbon storage. However, the proportion of FA and HA was low (3–4 g kg−1, or 12–15% of TOC), suggesting a low degree of humification and a predominance of labile, easily degradable organic compounds susceptible to microbial mineralization and CO2 emission. CaCO3 content was also low (<1%), implying minimal potential for carbonate-derived CO2 release. These findings confirm that drying FLs represent transitional systems and may shift from carbon sinks to carbon sources under ongoing climatic change. They also emphasize the need for more focused research on these, until now, underestimated ecosystems.