This study provided the first data on fish and amphibians diversity in Croatian karst springs. In order to determine fish and amphibians diversity in Croatian karst springs and, among them, the representation of species faced with a certain degree of extinction risk, but also endemic species, apart from descriptive statistics for the physical measures of certain species, I used diversity indices of fish and amphibians fauna of certain karst springs and geographic areas. Apart from traditionally used ecological indices that describe the diversity of an area, I also calculated the rarity index, the endangerment index and the combined biodiversity index. Values of all diversity indices of certain karst springs and geographic areas are very low due to the small number of isolated species. However, the central and the southern Adriatic Sea basin have a greater diversity than the Black Sea basin. According to the results of determining the high diversity areas, the southern Adriatic Sea basin springs have the highest indices values, especially the Norin spring. Because of the specific conditions in the karst spring areas not many species are able to adapt to such habitats. However, for some fish and amphibians species the karst spring areas are extremely important for their early development stages, which is confirmed by the results of this research. The species C. gobio, G. aculeatus, which is endangered species in Croatia, and the stenoendemic species of the Neretva river basin, K. radovici, are particularly emphasized among them.