John Smithson, Jennifer Peedom, Jo-anne McGowan and Joseph Nizeti claimed the award at the 12th annual Australian Academy of Cinema and Television Arts (AACTA) awards.
The film also won the AACTA Award for Best Original Score in a Documentary with Richard Tognetti, William Barton and Piers Burbrook de Vere claiming the prize.
The AACTA Awards (formerly the AFI Awards) have honoured screen excellence in Australia since the first AFI Awards were held in 1958.
Held annually in Sydney in recognition and celebration of Australia's highest achievements in film and television, the AACTA Awards present over 55 awards across two major ceremonies.
River explores the remarkable relationship between humans and rivers, taking its audience on an astonishing journey through space and time. Spanning six continents, and drawing on extraordinary contemporary cinematography, including satellite filming, the film shows rivers on scales and from perspectives never seen before.
This collaboration between Stranger Than Fiction Films and Arrow Pictures reunited the team behind the multi-award-winning feature documentary Sherpa.