The park is drained by tributaries of the Baza river, which is in the Guadalquivir basin. The permeable limestone landscape means that there is a lot of underground water, which flows out of the park's plentiful springs and fountains.
The main river is the Río Castril, home to a rich birdlife and many mammals, with many tributaries feeding into it. The park is dotted with many springs, such as Juan Ruiz, Tubos, Lézar and Magadalena, and waterfalls.