Mundaú river basin is located at Center-North Ceará State and occupies a total area of 2,227 km2, including Estuário do Rio Mundaú Environmental Protection Area. This study aimed to catalog the fishes of this basin. Collections were performed with active and passive gear in 35 sampling sites, between 2012 and 2014, in several habitats (main channels, streams, floodplains, permanent and temporary pools, ponds, and dams). A total of 2,545 specimens were collected, belonging to 55 species distributed in 10 orders, 31 families, and 50 genera; 30 of these are strictly freshwater species, and 25 estuarine-marine species. Three species (Hemigrammus guyanensis Gery, 1995, H. rodwayi Durbin, 1909 and Poecilia sarrafae Bragança & Costa, 2011) represent new records for the Mid-Northeastern Caatinga ecoregion. Besides, two cynolebiid species, Hypsolebias sp. and Anablepsoides cearensis (Costa & Vono, 2009), were found and the latter, currently classified as critically endangered, had its occurrence area widened.