The river rises below Mount Howitt on the western slopes of the Victorian Alps, within the Alpine National Park in the Shire of Mansfield.

[4] The Howqua River valley contains a number of archaeological sites of significance including at least two quarry sites for greenstone, an exceptionally hard rock used for stone axes, spears and other cutting tools which the Taungurung traded with other tribes.

[5] The character of Billy Slim in Nevil Shute's 1952 novel The Far Country was based on Fred Fry, a notable fly fisherman, who constructed several huts along the Howqua River and eked out a quiet existence in the river valley.

[7] In the Aboriginal Woiwurrung and Taungurung languages, the river is named Pyerlite, with no clearly defined meaning.

[2] There are four possible origins of the river's current name: firstly, after John "Howka" Hunter (1820–68), a pastoralist; secondly, a portmanteau name from Mount Howitt, where the river rises, and aqua; thirdly, after Howqua, a popular brand of Chinese tea in the early nineteenth century; and fourthly, after Akin Howqua (Ah Kin Wowqua), a Chinese surveyor and early resident of Melbourne.