Subterranean aquatic habitats may be of particular interest from the zoological point of view. Most of the studies dealing with aquatic troglobiont fauna focus on troglobionts, such as organisms spending their entire life cycle in caves. Few studies are dedicated to non obligate cave dwellers whose occurrence is usually considered as accidental or random. The focus of this paper is on identifying the role played by cave features in the occurrence of aquatic troglobiont fauna and assessing the relationship between species with and without troglomorphic features and their cave habitat requirements. Organisms' occurrence and environmental features were assessed during a repeated survey of all the caves occurring in a karstic valley of north-western Italy. We surveyed 39 natural caves from March to December 2013 sampling the waterbodies inside them for fire salamander larvae and invertebrates occurrence. 11 aquatic taxa were recorded during this study including 2 aquatic troglobiont species, Niphargus ambulator Karaman, 1975 and Dendrocoelum sp. n. All the taxa did not occur randomly. Aquatic troglobionts preferred deep and dark caves while other non obligate cave dweller occurred in shallower and brighter caves. The most important variables assessing distribution within caves were distance from the entrance and the temperature variation range of the pools. The occurrence of troglomorphic organisms was positively affected by pool distance from the cave entrance and pool area.