It winds through a generally steep and narrow course north, then west through the forested Klamath Mountains, but also passes through the Hayfork and Hyampom Valleys, which are the primary agricultural regions of Trinity County.
The Hayfork begins as two large springs, one rises on the west flank of Pine Root Saddle and the other on nearby Brushy Mountain some 7 miles (11 km) south of the hamlet of Wildwood.
Five miles (8 km) downstream, it enters the Hayfork Valley, a large agricultural basin in the middle of the Klamath Mountains.
[6] Winding northwest out of the valley, the creek enters a steep gorge, plunging over whitewater rapids and around giant boulders between narrow cliffs.
[7] Hayfork Creek drains a mountainous, remote watershed of 379 square miles (980 km2) situated entirely within southern Trinity County.
Although the majority of the basin is covered by the Klamath Mountains, it also contains some of Trinity County's only significant amounts of arable land in the Hayfork and Hyampom Valleys.
[10] The geography of the watershed is widely varied, from subalpine in the Chanchellula Wilderness and on Hayfork Bally down to hot, dry scrub and chaparral in the lower river valley.
Hayfork Valley consists mainly of oak and digger pine woodlands and grasslands, although much of this has been altered to accommodate housing and agriculture.
[12] Other towns within the basin include Peanut, which is located on Salt Creek, and Wildwood, situated near the headwaters of the Hayfork.
It is believed that the present course of the stream had been established prior to the formation of the mountains – as they rose, the creek's erosional force cut canyons and valleys into the bedrock, maintaining its course.
The Wintu established permanent winter camps on streams, and during the spring and summer traveled to farther and higher-elevation areas to hunt.
[21] The first outsider to see Hayfork Creek was fur trapper Jedediah Smith in the dawn of 1828, who was leading an expedition from northern California into Oregon.
[21] The route along lower Hayfork Creek that Smith and his men had taken later became a trade path between the Central Valley and coastal Oregon.
[21] In 1852, a settler from Weaverville, a town situated about 15 miles (24 km) northeast of the Hayfork Valley, was reportedly killed by Native Americans and his herd of cattle stolen.
Agricultural runoff since the late 1800s has hurt the ecosystem of the creek downstream of Hayfork, which is the largest farming region of the watershed.
[16] There are several species of endangered or threatened animals that live within the watershed, including the Northern spotted owl and peregrine falcon.
The geology of the stream bed is described as a "natural gold trap" and recent strikes have been made there of up to 60 ounces in one day.
[27] For experienced kayakers and rafters, the upper and lower thirds of Hayfork Creek are filled with rapids ranging from Class III to V. Especially in the lower portion of the creek, large boulders and waterfalls require strenuous portages; and high flow fluctuations (the river has no dams and only a few diversions) cause the stream to range between 50 cubic feet per second (1.4 m3/s) and 10,000 cubic feet per second (280 m3/s) in any given year.