Habitat specialists and generalists are known to differ in their width of environmental tolerance and their representation can vary along with the ecological contrast of habitats. In this study we explore factors shaping patterns of species richness and abundance of aquatic macroinvertebrate habitat specialists and generalists at isolated spring fens, separately for spring patch and spring brook mesohabitats at each site. We also examined habitat contrast of these unique island-like communities by the comparison of spring fen specialists and habitat generalists shared between the two spring fen mesohabitats and the nearest stream to each of 13 selects fen sites. Aquatic macroinvertebrates (Clitellata, Ephemeroptera, Plecoptera, Trichoptera, and Diptera) were investigated at 62 isolated spring fens, with 357 taxa identified in more than 172,000 individuals collected. We found that specialists experienced a stronger relation to local environmental conditions (i.e. the amount of dissolved oxygen and water conductivity) at both spring mesohabitats than generalists, primarily responding to fen habitat size. In contrast, responses of species abundances at spring patches and spring brooks differed as the abundances were controlled by the amount of oxygen in spring patches and by habitat size in spring brooks. Based on Trichoptera and Diptera assemblages we found a similar contrast between both spring fen sites and nearby streams. Our results suggest a higher resilience of specialist populations in well oxygenated sites and their competitive advantage over generalists at these sites, which stresses the importance to prevent any significant decrease of oxygenation (e.g., by eutrophication or drainage), especially in spring patches.