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 Cape Fear watershed headwaters are in the Piedmont geographic region characterized by relatively low, rolling hills extending into the Upper Coastal and Lower Coastal plains characterized predominantly by wetlands in the middle to southeast portions of the watershed. Elevations range from 900 feet in the western hills to sea level at the mouth of the Cape Fear River in Wilmington. Average annual precipitation in the Cape Fear watershed ranges from 42 inches in Greensboro near the head waters to 57 inches in Wilmington on the coast. The Greensboro area average annual snowfall of 9 inches. However, runoff due to snowmelt is generally not a concern in this watershed.

Within the Cape Fear basin, there is one USACE reservoir project. The project is the B. Everett Jordan Dam and Lake on the Haw River approximately 4 miles upstream of the confluence of the Deep River which creates the Cape Fear River. The project purposes include flood control, water supply, recreation, fish and wildlife enhancement, and augmentation of low flows for the purposes of pollution abatement and water-quality control in the Cape Fear River Basin.

Other locks and dams on the Cape Fear River include Buckhorn Lake Dam, Huske Lock and Dam, Lock and Dam #1 and Lock and Dam #2. Buckhorn Lake Dam creates a backwater effect at the tailrace of the B. Everett Jordan Dam. The Shearon Harris Lake Dam is located on Buckhorn Creek and serves the Shearon Harris Nuclear Power Plant, Unit 1 located in New Hill, NC. The plant is operated by Carolina Power & Light Company.

A few of the notable tributaries to the Cape Fear River include Turnbull Creek, Harrisons Creek, Rockfish
Creek, Little River, Upper Little River, Buckhorn Creek, Deep River and Haw River. Tributaries to the Haw River upstream of the B. Everett Jordan Dam include New Hope River, Cane Creek, Big Alamance Creek, Back Creek, Stony Creek, and Reedy Fork.

The key inflow gages in the basin include Haw River at Haw River, Haw River near Bynum, Morgan
Creek near Chapel Hill and New Hope Creek near Blands. Key gages downstream of B. Everett Jordan Dam are Deep River at Moncure, Cape Fear River at Lillington and Cape Fear River at Fayetteville.

During flood control operations, the primary objective of B. Everett Jordan reservoir is to control floods along the Cape Fear River, particularly in the vicinity of Fayetteville. The basic plan of operation is to maintain a normal pool elevation of 216 feet, mean sea level (msl), by releasing inflows up to nondamage stages in the downstream reaches of the river. The non-damage stage at Fayetteville is 31 feet at the river gage. The effects of runoff from uncontrolled drainage areas on Fayetteville stages is forecast by monitoring flows at the Deep River at Moncure gage, the Cape Fear River at Lillington gage and the Cape Fear River at Fayetteville gage. Flows from the Deep River are particularly significant.

An objective of water quality control at B. Everett Jordan Lake is meeting the North Carolina and Environmental Protection Agency (EPA) standards for both the impounded water and the river water below the dam. For low flow regulation, 94,600 acre-feet (67%) of water quality storage is reserved in the conservation pool of Jordan Lake for release during critically dry periods. 45,800 acre-feet (33%) of the conservation pool storage is reserved for water quality. A required minimum instantaneous flow of 40 cfs is maintained immediately below the dam. Releases are made from the conservation pool storage allocated to water quality as necessary to maintain a minimum of 600 cfs as measured at the Lillington stream gage. Occasionally, the flow at Lillington may drop below 600 cfs because of variations in river flows induced by small hydroelectric plants located on the Deep River.