•Due to climate change the surface of floodplain water bodies decreases substantially.•The share of small lakes and ponds increases.•Small floodplain lakes may be a substantial source of CO2 emission.•Carbon is buried mostly in insoluble forms. Small floodplain lakes (SFLs), characterized by their diminutive size (<10,000 m2), have been consistently overlooked in assessments of organic carbon (C) stock and the impacts of climate changes. This study aims to ascertain both the quantity and quality of carbon stored within the sediments of SFLs. Furthermore, we endeavour to evaluate the influence of ongoing climate change on the floodplain lake structure within the continental humid climate zone on the example of the Vistula River valley and estimate the CO2 emission from dry floodplain lakes. The sedimentary organic carbon content (TOC) ranged from 2.3–64 g kg−1, averaging at 3.4 g kg−1. Consequently, the sediments in the analysed SFLs of the river section potentially harbour up to 5,785 Mg TOC. Notably, the abundance of easily soluble carbon fractions (humic and fulvic acids) was relatively low (∼15 %), implying a stable immobilization of organic C compounds and minimal impact of sediments on water quality. Satellite imagery analysis for the years 2017–2020 revealed a 31 % reduction in the total lake surface area within a 100-km-long segment of the Vistula River. The decreasing surface area of floodplain lakes and rising mean air temperatures increase CO2 emissions and have an additional impact on climate warming. Our research underscores that investigating lake C storage concerning climate change demands a nuanced approach. While higher temperatures stimulate primary production, the reduction in lake surface area and the escalating role of small lakes, such as SFLs, in C storage should be paramount considerations.