Abstract In a time of rapid environmental changes, identification of the effects of climate warming on charophytes (Characeae, Charophyta) will enable the optimization of conservation measures, especially for extremely rare species. Lychnothamnus barbatus is one of the rarest charophytes worldwide, which has decreased in the number of occupied sites over the last century. However, the recolonization of former sites has been observed in recent years (e.g. Lake Kuźnickie, Poland). The study aimed to analyse the effects of climatic changes and human pressure on the L. barbatus population. Three 30 cm sediment cores were collected from minimum, average, and maximum depths of L. barbatus occurrence to determine the past vegetation composition. Sediment cores were dated using the radioisotopes lead‐210, caesium‐137, and carbon‐14. A spatial analysis of the lake catchment changes during the last 120 years was also conducted. The study demonstrated L. barbatus presence in Lake Kuźnickie at the beginning of the 16th century. However, a sharp increase in the proportion of this species in the vegetation community occurred in the 19th century and during climate warming at the end of the Little Ice Age. Factors that significantly influenced the present occurrence of the L. barbatus population included improvement in water quality and the oospore bank deposited in the bottom sediments. This study is the first palaeoreconstruction in a modern lake dominated by L. barbatus. Based on the history of L. barbatus in Lake Kuźnickie after the end of the Little Ice Age, the positive effect of climate warming on the contemporary recovery of this charophyte is postulated. The reaction of L. barbatus to climate warming appears to differ from commonly accepted scenarios for aquatic macrophytes because its recovery in the past and at present coincided with increases in air temperature. This research indicated the appropriate management and conservation practices for lakes with L. barbatus populations.