The dataset contains information on the content of inorganic carbon, organic carbon, humic substances, fulvic acids, humic acids, and carbonates in bottom sediments of small floodplain lakes within the Vistula River Valley, as well as in soils that have developed from these sediments. Sampling and analyses of organic carbon content were conducted within the framework of the project Miniatura 6 – “Climate change and the transformation of non-toxic sediments into toxic soils” (2022/06/X/ST10/00506), funded by the National Science Centre, Poland. The dataset contains extended carbon-related data for 8 out of the 12 lakes studied within the Miniatura 6 project. It includes both data generated as part of the project and additional, complementary measurements collected afterwards. The original and complete dataset is available at DOI 10.5281/zenodo.8384451.