The Applegate sub-basin is the 770-square mile watershed of the 51-mile long Applegate River, a tributary to the Rogue River. The headwaters of the Applegate River are in the Red Buttes Wilderness on the Siskiyou Crest just south of the Oregon border in Siskiyou County, California. As it flows towards its confluence with the Rogue the Applegate passes through Jackson and Josephine Counties in Oregon. It empties into the Rogue River west of Grants Pass at the beginning of the Wild and Scenic section of the Lower Rogue. The river is impounded behind Applegate Dam just inside the Oregon border creating Applegate Reservoir, which was built for flood control in the late 1970s, and today is used largely for recreation.
Much of the land in the upper reaches of the watershed is steep mountainous terrain managed by the Rogue River-Siskiyou National Forest; mid elevations contain a lot of Medford District BLM land and private timber lands, and the banks of the river are primarily rural private properties and small farms. The USFS, BLM, timber and private properties make up 35%, 35% 10% and 20% of the watershed respectively.
Major tributaries to the Applegate include Carberry, Elliot, Thompson, Williams and Slate Creeks as well as the Little Applegate River. Towns within the watershed include Ruch, McKee Bridge, Applegate, Williams, Provolt, Murphy and Wilderville, none of which are incorporated. All told the watershed is home to approximately 12,000 people.
Issues that Rogue Riverkeeper works on in the watershed include pollution from the Blue Ledge mine, degraded logging roads bleeding sediment into the streams and addressing recurring blowouts on a Talent Irrigation District ditch that dump sediment into the Little Applegate River.