The Corps Water Management System (CWMS) includes four interrelated models to assist with water management for the basin:

- GeoHMS (Geospatial Hydrologic Modeling Extension)
- ResSIM (Reservoir System Simulation)
- RAS (River Analysis System)
- FIA (Flood Impact Analysis)

Within the Rogue River watershed, Lost Creek and Applegate Lakes are operated by the USACE’s Portland District. The primary purposes of the Lost Creek Project are flood control, fisheries enhancement, irrigation and municipal and industrial water supply. In addition to these purposes, there are secondary objectives of providing hydropower production, wildlife enhancement, recreation, and water quality control. Lost Creek Lake provides drainage control for 28% of the Rogue River Basin above Grant Pass. The primary purposes of Applegate Lake are flood control, fisheries enhancement, and irrigation. Secondary purposes are recreation, wildlife enhancement and water quality control. However, storage is not allocated specifically for these secondary purposes. A third project, Emigrant Lake, is operated by the US Bureau of Reclamation for flood control. Portland District oversees flood control operations at Emigrant Lake under Section 7 of the Flood Control Act of 1944. Four diversion dams upstream of Lost Creek Lake divert water from Rogue River for power production. Murphy Dam and Mckee Dam downstream of Applegate Lake on Applegate River divert water from Applegate River for irrigation use (for more information see the Lost Creek Lake, Applegate Lake, and Emigrant Lake Water Control Manuals).

Within the Rogue River watershed, there are four geologic provinces: the High Cascades, Western Cascades, Klamath Mountains, and Coast Range. The headwaters of the Rogue River Basin reside primarily within the High Cascades and Western Cascades provinces. The High Cascades geologic province is characterized by highly permeable Pliocene and Quaternary lava flows that typically generate low rates of surface water runoff. The Western Cascades geologic province is characterized by Tertiary volcanic and volcanoclastic rocks that are generally weathered and highly dissected and, thus, generate relatively high rates of runoff. Most of the Rogue River watershed, including its largest tributaries, the Illinois and Applegate Rivers, reside within the Klamath Mountains geologic province. This province is underlain by an amalgamation of Paleozoic and Mesozoic terranes. A small section of the watershed near the confluence of Illinois River and Rogue River is within the Coast Range geologic province. This province consists of Eocene-age marine sedimentary rocks deposited on top of the thrust-faulted metamorphosed rocks of the Klamath Mountains geologic province (USGS, 2016).