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 drainage area above Alamo, approximately 4,770 square miles in size, is generally mountainous, and lies in west-central Arizona. The drainage area is bounded on the north by the Cottonwood Cliffs; on the east, by the Juniper and Santa Maria Mountains; on the south by Date Creek and the Harcuvar Mountains; and on the west by the Hualpai Mountains.

The Bill Williams River is formed about 47 miles upstream from its mouth by the confluence of the Big Sandy and Santa Maria Rivers. From the confluence, the flow is southwest for about 8 miles on an average gradient of 18 feet per mile to Alamo Dam. Bullard Wash is the largest tributary along this reach.

Below Alamo Dam, the river flows almost due west to its confluence with the Colorado River. The Big Sandy River, the larger of the two main tributaries to the Bill Williams River, drains an area of about 2,840 square miles. This stream, which is formed by the confluence of Trout and Knight Creeks, flows southward about 49 miles on an average stream gradient of 38 feet per mile to its confluence with the Santa Maria River. Burro Creek is the largest tributary in this reach.

The Santa Maria River drains an area of about 1,550 square miles. This stream, which is formed by the confluence of Kirkland and Sycamore Creeks, flows southwestward about 51 miles to its junction with the Big Sandy River. The stream gradient of the Santa Maria River is about 30 feet per mile. Date Creek is the largest tributary in this reach. The streambed gradients of many of the minor upstream tributaries in the Bill Williams River system are greater than 100 feet per mile.

The drainage area consists essentially of broad desert valleys and irregularly distributed ranges of rugged mountains. Relief is moderate to high. Elevations in the drainage area vary from about 990 ft above sea level at the base of the dam to 8,226 ft at Hualpai Peak on the northwest boundary.

The Bill Williams River is a perennial stream, although subterranean in some reaches. The longest segment is between Lincoln Ranch and Planet Ranch, a distance of approximately 23 river miles.
The climate is typically desert in character over the lower elevations of the basin, with short, mild winters and long, hot summers. In the higher elevations, the summers are milder, and the winters are colder and longer. The Alamo Basin has two distinct rainfall seasons: winter and summer, with a dry fall and a very dry late spring. The heaviest precipitation occurs in the summer, with about one-third of the annual precipitation normally occurring in July and August and one-half during the fall and winter months. The driest time of the year is later spring.