The study analysed three wetlands located in eastern Poland which have been subjected to varying levels of anthropogenic pressure, and conservation measures over the years (Bagno Bubnów, Krowie Bagno and Ostoja Poleska). They are the remnants of the primaeval wetlands, of Western Polesie. The objectives of this study were to: analyse the long-term changes in the frequency of occurrence of plant communities and rare plant and bird species from 1950 to 1970 (before protective measures were implemented) to 2000–2020 (when protection was in place); assess the changes of the climatic and edaphic habitat conditions during the half-century of transformation processes, using ecological indicators; and indicate the least and most transformed among the analysed areas. The wetlands of western Polesie constitute a sanctuary of great habitat and species diversity. The degree of deformation and the forms of protective activities significantly influenced the biodiversity of the analysed sites. The greatest changes in the occurrence of the plant communities and rare plant species during the half-century took place in Krowie Bagno, while the smallest in Bagno Bubnów. In all areas, the fertility of habitats increased and their humidity decreased. The downward trend is most pronounced in the declining bird populations observed across the studied areas. Strong anthropopressure (drainage) and late protection (Krowie Bagno) contributed to lower biodiversity. Our results confirm that low anthropogenic pressure and early protective measures mean an increase in the diversity of plant species and communities. Preserving the biodiversity of these naturally priceless areas is the priority. The results show that the necessary condition is to stop water loss from these areas. The observed trends in plant communities and rare plant species indicate a high threat to the least transformed wetlands.