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)

The Skagit River basin is located in the northwest corner of the State of Washington. The Skagit River basin extends about 110 miles in the north-south direction and about 90 miles in the east-west direction between the crest of the Cascade Range and Puget Sound. The northern end of the basin extends 28 miles into Canada.

The Skagit River originates in a network of narrow, precipitous mountain canyons in Canada and flows west and south into the United States where it continues 135 miles to Skagit Bay. The Skagit River falls rapidly from its source at an elevation of about 8,000 ft to 1,600 ft at the United States-Canadian Border. Within the first 40-miles south of the International Border, the river falls a further 1,100 feet and the remaining 500 feet of fall is distributed along the 95 miles of the lower river. Downstream from Sedro-Woolley, the valley descends to nearly sea level and widens to a flat, fertile floodplain and delta with an east-west width of about 11 miles and a north-south width of about 19 miles. The floodplain and delta joins the Samish River valley to the north, and extends west through Burlington and Mount Vernon to La Conner, and south to the Stillaguamish River. Between Sedro-Woolley and Mount Vernon, a large area of floodplain provides natural storage, primarily in the lower Nookachamps Creek Basin along the left overbank of the Skagit River. For very high river flows, a portion of the Skagit River in this reach can overflow the right bank and escape out of the system through Burlington to Padilla Bay and to Samish Bay. This overflow area is commonly referred to as the “Sterling Spill.”

The Skagit River continues through a broad outwash plain in the lower reach nearest the river mouth and divides between two principal distributaries, the North Fork and the South Fork, which are approximately 7.3 and 8.1 miles long, respectively. About 60 percent of the discharge is carried by the North Fork and the remainder is carried by the South Fork during lower flows, but this split becomes closer to 50-50 for higher flows.

The upper basin is mountainous, largely forested, and sparsely populated. Almost 90 percent of the upper basin is either designated as national forest or national park (Ross Lake National Recreation Area and portions of the North Cascades National Park and the Mt. Baker Snoqualmie National Forest). There are three major tributary rivers to the Skagit: Sauk-Suiattle, Cascade, and Baker. The Sauk-Suiattle and the Cascade Rivers are designated as wild and scenic and their flows are not controlled by dams or other structures. The Upper and Lower Baker Dams (together, the Baker River Hydroelectric Project) located on the Baker River are owned and operated by Puget Sound Energy (PSE), a private power utility. The USACE is authorized to use flood control storage in Upper Baker Dam. Ross Dam is located on the Skagit River and owned by Seattle City Light (SCL), a public power utility. The USACE is authorized to use flood control storage in at Ross Dam.

In the lower basin, the Skagit Valley, the 100,000-acre valley area downstream from the town of Concrete, contains the largest residential and farming developments in the basin. The 32-mile long valley between Concrete and Sedro-Woolley is from 1 to 3 miles wide, with mostly cattle and dairy pasture land and wooded areas. The valley walls in this section are steeply rising timbered hills.

In a large flood, the majority of the potential economic damages and potential threats to life safety would be located in the Skagit River floodplain, downstream of the city of Sedro-Woolley (population 11,000) in the cities of Burlington (population 8,700) and Mount Vernon (population 32,100). Critical infrastructure in Sedro-Woolley includes State Routes (SR) 9 and 20 (critical local access routes), United General Hospital, the Sedro-Woolley wastewater treatment plant, and a Life Care assisted living facility. Critical infrastructure in and around Mount Vernon and Burlington includes Interstate 5, Burlington Northern Santa Fe (BNSF) Railroad, SR 20, SR 9, and SR 536), numerous water and gas pipelines, light industry, and municipal infrastructure. The cities and critical infrastructure in the lower basin are protected by a system of levees and reservoirs along the Skagit River, while in the upper basin, levees are limited to areas surrounding critical locations.