[4] Four springs in the San Francisco Peaks originate the river; they would not produce enough water to maintain flow if not for the heavy rain and snowfall of the area supplementing the levels in the channel.

[9][10] During the Sitgreaves Expedition multiple new species were discovered at the spring, including Abert's squirrel, the Western Pocket Gopher, and Woodhouse's toad.

During the 20th century, the springs had been modified and sequestered to provide water for the city and for different private owners, with underground pipes particularly reducing the flow.

The river continues south through downtown Flagstaff, with the Frances Short Pond having formed by Thorpe Park in the west of the city.

[4] The river did not always run its current course through the city, as during the 20th century it was rerouted in certain areas to allow urban expansion and as a means of flood control.

Within the urban areas, non-absorbent surfaces mean that unfiltered rainwater is entering the river, which can contain pollutants poisonous to fish.