Human activities affect even the most remote and best preserved places on Earth. One of those places is Dalhousie Springs, Witjira National Park, in the arid centre of Australia. In 2003 we resurveyed the fish communities in springs to document changes since an earlier survey in 1991. Over the 12 years there were 18 population extirpations and only two colonizations, so total occurrences of five native species in 30 springs decreased from 83 to 67 populations. One species, the endemic Dalhousie goby, Chlamydogobius gloveri, accounted for 12 of the 18 population extirpations. Each fish species tended to persist in springs larger than some threshold size. Extirpations were related to spring size, with smaller springs more readily loosing populations, and to major habitat changes, which included large increases in the tropical reed Phragmites and concomitant decreases in open water, disturbed habitats, and dissolved oxygen. Extirpations of fish populations can be attributed primarily to habitat changes associated with reduced disturbance and herbivory as a result of the removal of feral livestock. These changes highlight the keystone impacts of large mammals on habitats and biotas of desert springs, and should be considered in management practices and policy decisions.