The number of threatened freshwater fish species in Spain is among the highest recorded in Europe and includes a high percentage of endemic taxa. We investigated the distribution of Spanish freshwater fish to identify priority areas for conservation and assess the extent to which freshwater fish are included in the existing network of protected areas. We considered those threatened species recorded in the Spanish National inventories. From these data, several biodiversity indices were calculated and analysed. Our results reveal important discrepancies between the national and international assessments of conservation status. The current Spanish national catalogue requires updating to reconcile these inconsistencies. Several important areas for the conservation of freshwater fish lie outside protected areas. Our results encourage the establishment of protected areas specifically for freshwater environments. An extensive database of Spanish freshwater fish species is needed to redefine priority areas and to maintain freshwater biodiversity.