The river was said to have been named by Spanish explorer Gabriel Moraga in 1806 when he found many skulls of Native Americans along its banks.

The Stanislaus River is named for Estanislau, a coastal Miwuk who escaped from Mission San Jose in the late 1830s.

He is reported to have raised a small group of men with crude weapons, hiding in the foothills when the Spanish attacked.

The Calaveras makes a northerly arc, passing through farmland, orchards, and the University of the Pacific Stockton Campus, then alongside its namesake Brookside district, before flowing into the Deepwater Channel about three miles downriver from the Mormon Slough.

Thus much of central Stockton, being completely surrounded by these waterways, is itself one of the many river islands which make up the San Joaquin Delta.

[8] The Calaveras River has various species of fish that people catch, eat, and even some that are federally protected such as steelhead and rainbow trout.

Per-and Polyfluoroakyl substances (PFAs)  are man-made chemicals designed to make products stain and water resistant, but are of concern to the environment because of their difficulty to be decomposed.

Since learning about the effect of pesticides, farmers have started to reduce the use of them either by switching to more organic options, diluting the chemicals, etc.

Producing toxins, blocking sunlight by dense blooms and potentially using up all the oxygen in the water are many ways in which aquatic life is harmed.

In 2020, the Stockton East Water District planned out a program that would protect the threatened Central Valley steelhead, endangered Chinook salmon, and more natural wildlife.