It drains a watershed of more than 700 square miles (1,800 km2) on the west side of the Sacramento Valley in Glenn, Colusa, Lake and Tehama Counties.

[10] It continues in a generally northward direction for about 20 miles (32 km) through various parallel north-south ridges and sedimentary valleys of the Coast Range foothills.

[12] Below the dam it receives Briscoe and Elk Creeks from the left, and is crossed then paralleled for several miles by California State Route 162.

[20] The Stony Creek watershed consists of 777 square miles (2,010 km2)[2] mostly in the Coast Range foothills and a smaller area of the Sacramento Valley.

[20] Black Butte Lake has also suffered water quality issues, with a toxic blue-green algae bloom occurring most recently in summer 2017.

[22] Agriculture makes up most of the local economy, with the major crops being almonds, olives, oranges, wheat, and corn, and also dairy operations and pasture.

[20] Nearly all of Stony Creek's course is in Glenn County, where the landscape is divided into two major terranes, or crustal fragments that have accreted to the North American continent over millions of years.

[25] To the west is the Coast Range terrane, composed of folded, faulted marine rock from the Jurassic and Cretaceous periods (about 200–65 million years old).

[22] The Stony Creek Formation, composed mainly of conglomerate, sandstone and shale, is found further east in the foothill transition zone between the Coast Ranges and Sacramento Valley.

[26] The Sacramento Valley terrane to the east is composed of sedimentary rock overlain by thick layers of fluvial sediments, mainly clay, gravel, sand and silt.

[22] While the native grasslands and riparian habitats of the Sacramento Valley have been almost entirely replaced by agriculture, the foothill and mountain areas of the Stony Creek watershed have a diversity of plant communities.

[22] Upper Stony Creek is home to a variety of native and introduced fish species, including rainbow trout, hardhead, bass, catfish and carp.

[20] Historically, anadromous fish (salmon and steelhead migrated from the Pacific Ocean, and up the Sacramento River and Stony Creek to spawn.

[20] Historically, lower Stony Creek was a braided stream with a wide rocky bed, replenished each year by large volumes of sediment eroded off its watershed.

[20] As a result, the creek bed has become narrower and deeper, reducing spawning habitat for salmon and creating ideal conditions for invasive giant reed (arundo) and tamarisk.

[22] In addition, there is a proposal to dredge gravel that has accumulated in Black Butte Lake and use it to replenish the streambed, improving habitat for native fish.

[29] In dry years, when forage was scarce at lower elevations, thousands of natives migrated to temporary settlements along upper Stony Creek.

"[31] The following year, General John Bidwell explored Stony Creek from a point west of Colusa down to its mouth, for the purposes of locating suitable land grants for settlers.

[6] Fur trappers soon came to the area to catch beaver, which at the time were plentiful on Stony Creek, but they got into trouble with the Native Americans there and retreated in haste.

Uriah P. Monroe salvaged the remains and used the lumber to build the Monroeville hotel, which became a popular stop along the main Sacramento River road.

Small amounts of copper, ochre, manganese, marble, mercury, dimension stone and coal have also been mined in the Stony Creek watershed.

[33] The town of Orland was founded in the early 1870s when the Southern Pacific Railroad reached the area, and soon became a major grain processing and shipping center.

Early dry-land farming by Glenn and others had the effect of damaging local soils; wheat yields fell considerably by the 1890s, after which cattle ranching became dominant.

Stony Gorge Dam was completed much later, in 1926, after a severe drought convinced local water users to finance a second reservoir.

[38] Reclamation relinquished project control to the Orland Unit Water Users' Association in 1954, and the government bonds were finally repaid in full in 1989.

[44] The earth-filled Black Butte Dam was constructed in 1963 by the U.S. Army Corps of Engineers and is the main flood control facility for lower Stony Creek.