Abstract Trapa natans (water chestnut) is an aquatic, thermophilic plant whose decline has been observed in many localities in central Europe during the last decades. In this paper, we present a description of two new T. natans subfossil sites located outside its present northern distribution in Poland. High-resolution analysis of plant macrofossils supported by geochemical analysis were undertaken to reconstruct the palaeoecological habitat and examine the cause of the late Holocene decline of T. natans that took place ca. 4000 calibrated years before AD 1950 (cal. yr BP) in a paleolake, presently the Bagno Kusowo bog. Its disappearance was a consequence of terrestrialisation and the development of peatland. In paleolake sediments covered by the peat layer in the Mechacz Wielki bog, T. natans macrofossils were found from before ca. 3300 cal. yr BP. The decline of T. natans could have resulted from the changes and development of other plant communities where the dominant role was played by Stratiotes aloides and Nymphaea sp. In our study sites, T. natans occurred together with Potamogeton crispus, Potamogeton obtusifolius, Nymphaea alba, and Nuphar sp. in eutrophic water dominated by Ca2+, Fe3+, and Al3+ ions. Our palaeobotanical and geochemical results align with the contemporary conditions of T. natans habitat.