Few studies have focused on non-troglomorphic fishes occurring in Brazilian caves, especially those in the Caatinga region. The present study is the first survey of fishes from karstic areas of the Jandaíra Formation in Rio Grande do Norte State, northeastern Brazil. This region is characterized by a high concentration of caves and a rich subterranean biodiversity, especially of troglobitic invertebrates, but remains considered a gap on the knowledge of the subterranean ichthyofauna in Brazil. Four field expeditions were carried out covering two dry and two rainy seasons, in 2018 and 2019, in 23 localities in small river basins along the western part of the Jandaíra Formation. A total of 829 fish specimens, none of them troglomorphic, was captured and identified as belonging to 25 species of 12 families and five orders. Amongst them, four species are endemic of the Mid-Northeastern Caatinga ecoregion, and two non-native species were recorded. Habitats were classified into three categories: superficial, associated to cave, and cave. Although no troglomorphic fish species was found in this study, we recorded 64.1% of the Apodi-Mossoró river ichthyofauna occurring in caves or associated to caves, corroborating the hypothesis that part of the ichthyofauna exploits these environments as a refuge during the dry season. In addition, we suggest conservation policies for the maintenance of subterranean and aquatic semiarid ecosystems in the Jandaira formation, which is currently under threat due to anthropogenic activities, such as mining and deforestation.