The perennial flow in Surprise Canyon supports extensive riparian habitat and one of the most diverse and significant wildlife communities in the California Desert. This habitat is home to a rich assemblage of more than 70 bird species as well as the rare Panamint alligator lizard, which inhabits the canyon’s rocky bottom near permanent water and riparian vegetation. Surprise Canyon is also an essential source of water for the desert bighorn sheep population in the Panamint Mountains. Limestone outcrops in Surprise Canyon provide micro-habitat for several sensitive plant species, including the Panamint dudleya and the Death Valley round-leaved phacelia.
The 2019 John D. Dingell Jr. Conservation, Management, and Recreation Act protected 7.1 miles of Surprise Canyon as a National Wild and Scenic River.