The developmental history of shallow, eutrophic Lake Głębokie Uścimowskie, eastern Poland, spanning the last 180 years, was studied using analyses of pollen, plant macrofossils, diatoms, chlorophyll and carotenoid pigments, Cladocera, Chironomidae and geochemistry from lead-210 dated sediment cores. The lake was colonised by macrophytes and eutrophic through the whole investigation period, but from 1950 AD the trophic status increased slowly and eutrophication accelerated after 1980 AD, leading to hypertrophy. Despite this eutrophication history, macro- and microfossils indicated the continuing presence of Isoëtes lacustris spores and Elatine hydropiper seeds in the sediments of the lake, even though neither species were encountered in the recent and present-day lake macrophyte surveys. Both the species are classified as vulnerable (IUNC List) in Poland and are presently deemed extinct due to eutrophication in the Łęczna-Włodawa Lake District. We conclude the silica-rich substrates (51–77%), low in calcium (<1%) and organic matter (7–21%) in the lake were crucial for the survival of soft-water species like I. lacustris and species that prefer sandy littoral habitats like E. hydropiper. We also propose that water level fluctuations were important in modifying the extent of the littoral zone and sorting the substrate and thus in maintenance of appropriate habitat for these rare species. Therefore, substrate type and hydrological factors appear to be important to conservation of rare species in this lake.