Whiskeytown supports abundant and diverse animal assemblages, which reflect the numerous vegetation communities in the park. Through the Klamath Network Inventory and Monitoring program, wildlife inventories have been completed to document bird, small mammal, amphibian, reptile, and bat species in the park. Four federally threatened wildlife species, one federal candidate species, twelve federal species of concern, one California threatened species, and ten California species of concern have been documented so far in Whiskeytown.
Bird watching and wildlife viewing are popular activities at the park, and visitors are encouraged to participate in these activities in a safe and respectful manner. Whiskeytown is home to mountain lions, black bears, and rattlesnakes and appropriate precautions should be taken when encountering these animals.