Clearwater Documentary was initially incorporated as Clearwater Media by Tom Radford in 1998. As Clearwater Media, the production company created documentaries with a specifically Canadian focus with particular emphasis on Arctic and western exploration. Notable productions created under the Clearwater Media banner include I, Nuligak, Alberta Bound, Arctic Dreamer, and The Great Divide.

Anthropologist Niobe Thompson joined Clearwater Media in 2006 as a director of development and in 2008, Radford and Thompson launched Clearwater Documentary. This new production company broadened its perspective to a global scale and began producing documentaries with a focus on environmentalism, evolution, physical anthropology, and energy. Notable productions created under the Clearwater Documentary banner include The Great Human Odyssey, Tar Sands: Canada for Sale, and Tipping Point.