Like the rest of the Sierra Gorda region, Pinal de Amoles is marked by very rugged terrain, which includes canyons and steep mountains. The area is located in an area with extremely high peaks with small flat areas and mesas. The altitude varies between 839masl at the community of Huajales to 3350masl at the Cerro de la Calentura, which is also the highest point in the state. Eighty eight percent of the municipality's territory belongs to the Sierra Gorda Biosphere Reserve of Querétaro, a region which is protected because of its extreme diversity of landscapes, climates, vegetation and wildlife. Pinal de Amoles represents the highest peaks of this region, which essentially separate the wetter lands to the north and east from the semi arid areas of the south and west as the mountains block moisture coming in from the Gulf of Mexico. Most of the rock is sedimentary, with about 45% limestone. About 15% is intrusive volcanic rock. This due to the fact that much of the Sierra Gorda was sea bed millions of years ago, with volcanic activity later in its geological history. The volcanic rock accounts for most of the municipality's minable deposits.