Springs, as unique ecotonal habitats between surface and hypogean areas, are considered endangered aquatic ecosystems due to direct and indirect human impacts and climate change issues. They are distinctive water habitats that are often inhabited by a diverse but mostly stenotypic group of organisms. The present study considered 31 springs from the Apuseni Mountains (the Romanian Carpathians) that were classified as rheocrene, helocrene, and limnocrene based on their geomorphology and hydrology. Samples from three substrate types (rocks, sand, and bryophytes) were collected using standard methods for crenic invertebrates. A total of 64,462 individuals belonging to 17 invertebrate taxa were identified: aquatic worms, mollusks, crustaceans, water mites, and insects. Amphipoda and Diptera–Chironomidae were the dominant taxa in most springs. At a community level, patterns of habitat preference were demonstrated for 12 invertebrate groups using the standardized selection index (B) and expressed as the number of springs where a certain group selected rocks, sand, and/or bryophytes: Four groups exhibited preferences for bryophytes (Coleoptera, Diptera, Plecoptera, and Trichoptera), Ephemeroptera exhibited preferences for rocks, and Copepoda exhibited preferences for sand. Amphipoda, Platyhelminthes, and Ostracoda displayed preferences for all three substratum types, while Gastropoda, Hydrachnidia, and Oligochaeta recorded lower percentages in springs where habitat preferences were significant. In addition, crenic invertebrates were divided into three guilds, depending on their dispersion abilities in any stage of their life cycle: sedentary (not-winged groups), mobile (winged groups), and ectoparasites (water mites that were able to leave the springs on their winged hosts). Sedentary taxa recorded higher percentages of abundances and habitat preferences towards rocks and sand, while ectoparasites (Hydrachnidia) and the mobile guilds tended to prefer bryophytes. This segregation might be explained by individual adaptations to the particularities of each type of substratum, such as the bodily form of the copepods, which are well suited for sand interstices, a habitat that our data showed that they preferred. Our results represent novel contributions to the knowledge of habitat preferences of spring invertebrates from the Apuseni Mountains, adding value to similar data from the Western Carpathians, the Alps, and the Dinaric region.