Central Calnali is located at 980 m elevation, and the entire municipality occupies the eastern slope of the Sierra Madre Oriental. The terrain is largely mountainous Veracruz moist forests fragmented by pasture and cropland. The Río Calnali and the Río Tula/Atempa, tributaries of the Río Conzintla and ultimately the Río Pánuco, traverse the municipality from west to east. Each of these rivers is a hybrid zone between two species of the swordtail fish Xiphophorus.