The river and its tributaries drain in
Trinity County in the south and
Humboldt County and Trinity County in the north and comprising 34 percent of the Trinity River watershed. The Hayfork Creek sub-watershed contains , or 38 percent of the entire South Fork Trinity watershed. Most of the watershed lies on public lands (79 percent), while for Hayfork Creek, 78 percent of its watershed lies on public lands. With the
Yolla Bolly Mountains in the south and the
Klamath Mountains in the north, the topography of the South Fork Trinity's watershed is dissected by deep gorges and valleys separated by narrow ridges. The South Fork is the longest undammed
National Wild and Scenic River in California.{{cite web While along the length of the South Fork itself there is little human development, it receives agricultural pollutants from Hayfork Creek, whose valley contains over of ranchlands and farmlands. In fact, there have been sightings of frequent
fish kills in Hayfork Creek and it is said to have "severe water quality problems in the summer".{{cite web Diversions off Hayfork Creek have only furthered the pollution problem by concentrating it. pollutants from marijuana farms and diversions are the two primary negative factors affecting the South Fork mainstem. Clearing hillsides has accelerated erosion, clouding the water and causing difficulties for
steelhead trout and
chinook salmon, which once spawned in the river in prodigious numbers. Much of the South Fork Trinity River's watershed is the
Shasta-Trinity National Forest, which covers most of the mountainous areas in the southern and central part of the watershed, and the
Six Rivers National Forest, which covers most of the northern third of the basin. Nearly the entire length of the South Fork above the Hayfork Creek confluence is inside the Shasta-Trinity National Forest, while below the confluence, national forest lands peter out into privately owned land and the river then enters Six Rivers National Forest. Most of the upper and lower Hayfork Creek reaches also are in the Shasta-Trinity forest, while a large amount of private land surrounds its middle reach in Hayfork Valley and the town of
Hayfork. Throughout nearly the entire watershed, there are sporadic patches of private lands and
Bureau of Land Management-owned lands.
Streamflow The river flows into the Trinity River northwest of
Salyer. The
United States Geological Survey monitors the South Fork Trinity River's flow at four gauges; these are at
Salyer, downstream of
Hyampom, at Hyampom upstream of the Hayfork Creek confluence, and
Forest Glen (from mouth to source).{{cite web The average flow of the river at its mouth is .{{cite web For Salyer, closest to the mouth, the highest peak flow was on December 22 in the
1964 flood, while the lowest was on 31 December 1954.{{cite web For the location downstream of Hyampom, the highest recorded peak flow was on 22 December 1964, while the lowest was .{{cite web For the location at Hyampom, the highest peak was on 22 December 1964, while the lowest was on 13 February 1962.{{cite web For Forest Glen, the largest peak was on 22 December 1964, and the lowest was on 13 February 1962.{{cite web ==History==