The caddisflies (Trichoptera) of calcareous fen habitats, in contrast to those of other peatland types, have been poorly researched. We thus conducted a two-year study in south-eastern Poland encompassing four types of such habitats—drained and undrained fens and water bodies (pools and ditches) located within the fens—in order to define trichopteran reference assemblages (PCoA), indicator species (IndVal analysis), and the drivers (both natural and those associated with landscape management, including area protection) responsible for caddisfly species distribution (CCA). The most important environmental driver was habitat persistence. Distance-based RDA analysis revealed a distinct pattern in the distribution of species with or without diapause along the persistence gradient. Environmental drivers associated with plants were also crucial for both fens and water bodies. The key factor influencing the caddisfly assemblages of pools and ditches was the use and management of the surrounding land, whereas in the fens, it was the level of area protection. Physical and chemical water parameters had no statistically significant impact on the assemblages. Some factors can be modified by humans (e.g., water level regulation, vegetation, and landscape management) to maintain healthy ecosystems for aquatic insects.