Heavy precipitation in the region feeds large streams that swell with winter rains and shrink during summer drought. The U.S.Geological Survey (USGS) estimates that at least 65 percent of the rainfall here eventually reaches the Eel River as runoff. A 5-kilometer reach (3 miles) of the South Fork of the Eel River winds through the reserve, and its flow fluctuates greatly. Extremes recorded since the early 1950’s range from a high flow of 20,000 cubic feet per second (CFS) in December 1955 to a low flow of 0.45 cfs in August 1977.

The upper reaches of the South Fork Eel River pass through a checkerboard of BLM and privately owned land. Downstream of the reserve, the river corridor is protected as part of the federal Wild and Scenic Rivers system. From Leggett to its confluence with the main stem Eel River at Fernbridge, approximately 160 kilometers (100 miles) downstream from the reserve, the South Fork is used heavily for recreation.

Watersheds free from dams and logging are rare in the Coast Range, yet three undisturbed watersheds are completely contained within the boundaries of the reserve. The Elder Creek watershed – at 16.8 kilometers (6.5 square miles), the largest of the three – is registered as a National Natural History Landmark by the National Park Service. In recognition of the water’s purity, the USGS operates a Benchmark Hydrological Station on Elder Creek, one of 57 benchmark stations throughout the United States. Hydrologic data have been collected here continuously since 1967. Fox Creek, another large perennial stream, has a watershed of 2.6 square kilometers (1.0 square miles). It dissects a river terrace near Wilderness lodge, where its water has been tapped for domestic use since the homesteaders’ time. The smaller Skunk Creek watershed provides the coolest channel and a very moist riparian zone for comparative studies. Additionally, there are numerous intermittent streams, springs, and seeps throughout the reserve.