The Hayfork Creek Watershed is 243,000 acres, 21.4% of which is privately held and the other 78.6% is federal lands, mostly U.S. Forest Service timberland. This watershed is the largest sub-basin of the South Fork Trinity River. Private land use in the Hayfork Creek Watershed is primarily timberland with 34,600 acres, grazing lands are the next largest land use with 10,000 acres, followed by pasture and hayland with 2,100 acres, and 1,000 acres considered urban. There are currently 18 active surface diversions in the watershed utilizing more than 9,870 acre feet of water per year. These diversions are mostly made from rock and plastic sheeting and are reconstructed each year. The earthen ditches used to convey the water to irrigated fields typically have an estimated 50% or greater loss rate due to seepage and evapotranspiration.

In this watershed the decline of the fisheries is due, in part, to low water flows, high water temperatures, and loss of habitat. The major causes of low water flow and high water temperatures in normal rainfall years are irrigation diversions, domestic water use, and loss of riparian vegetation from grazing and clearing, which has reduced stream shade. High water temperatures, septic effluent, and wastes from grazing animals decrease the dissolved oxygen (DO) levels. The cumulative effects of high temperatures, low DO, and concentrated contaminants stress the remaining salmonid populations.