Mystery Road: Origin was mainly filmed in Western Australia. The primary filming locations include the town of Kalgoorlie, the suburbs of Boulder, and the Coolgardie ghost town. Additionally, the opening scenes featuring salt lakes were filmed at Lake Lefroy, which is about an hour west of Kalgoorlie. For the second season, filming took place in the South West of Western Australia, particularly around Pemberton and its surrounding areas such as Deanmill, Big Brook Dam, and Yeagarup, featuring the region's distinctive karri trees and timber towns.

The Kalgoorlie area was chosen for its red desert terrain which suited the dry, dusty outback environment depicted in the series. The historical gold mining background of Kalgoorlie-Boulder and Coolgardie also played a role in setting the series' atmosphere. The second season's shift to the lush forests of Pemberton provided a new scenic backdrop reflecting a different part of Western Australia.