The municipality is located in the southern portion of the state in the Bajío region of central Mexico, and has an area of some 819.6 square kilometres (316.4 sq mi).

The city of Valle de Santiago lies at an elevation of 1,744 metres (5,722 ft) in the east-central part of the municipality, approximately 90 kilometres (56 mi) south of the state capital, Guanajuato.

Over 30 inactive volcanic craters are located in Valle de Santiago, but only 7 of those are recognized, and protected as they have been declared a national monument.

La Alberca, which translates to "the pool", was once an abundant lake that just over 40 years ago was filled with fresh water, but due to human activity has now dried up and been populated with cacti and shrubs.

One of the biggest factors for the current state of these now dried crater lakes is the over extraction of groundwater for both water supply and irrigation.