Over 450 distinct Native American structures have been recorded in the monument, some of large pueblos containing more than 100 rooms each.

Numerous ruins of agricultural terraces and irrigation devices indicate that farming was widespread during this period.

Other historical entities that are found include 19th century mining features and Basque sheep camps.

Notable species of reptiles and amphibians, including the leopard frog, the garter snake, and the desert tortoise, can be seen at the monument.

Native fish including the longfin dace, the Gila mountain sucker, speckled dace, and three endangered native fish including the Gila intermedia, charalito, and desert pupfish exist in the 129-mile (208 km)-long Agua Fria River and its tributaries.