In this paper, we discuss the threats to freshwater habitats that are highly important to the European Community in the Continental Biogeographical Region of Europe, specifically in Poland. The study covers nine freshwater habitat types distinguished in Natura 2000, Annex I of the Habitats Directive, which is a network of nature protection areas in the territory: standing water bodies (3110, 3130, 3140, 3150, and 3160) and running water (3260, 3220, 3240, and 3270), occurring in 806 Special Areas of Conservation in Poland. Of the 72,673 km 2 total area of freshwater habitat covered by Natura 2000 in Poland, only 25.70% was classified, from the period 2006-2018, as favourable status, whereas 68.72% was classified as unfavourable inadequate or unfavourable bad status. Based on a multivariate analysis, we found that significant differences in the conservation status of freshwater habitats resulted from a variety of threats, pressures, and activities, among which the most significant are urbanization and residential and commercial development; transportation and service corridors; decreased and unstable water resources; fishing and harvesting of aquatic resources; agricultural pollution; improper management and use of the agricultural catchment and forest catchment; changes in biocenotic evolution, invasive species succession, and more intense touristic exploration. The changes in conservation status of habitats 3110, 3130, 3140, 3160, and 3260 are also associated with climate change. Taking into account the threats identified, a list of recommended practices for the freshwater habitat types is presented, to be considered in habitat conservation programmes.