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 Mississippi River Basin is the largest river system in the United States, covering approximately 1.15 million square miles, or over 40% of the area of the Continental U.S. Several large tributary rivers flow into the Mississippi, including the Missouri, Ohio, and Arkansas Rivers. Maximum topographic relief varies from approximately 1,475 feet near the headwaters at Lake Itaska to 0 feet at the Gulf of Mexico. The portion of the Mississippi River Basin that is covered in this CWMS project drains approximately 15,475 square miles.

The Mississippi River in the St. Louis District covers a centerline distance of about 300 miles, flowing generally from the northwest to southeast, from Lock and Dam #22 in Saverton, MO to the mouth of the Ohio River near Cairo, IL. The topography of the basin is characterized by hilly upland terrain and broad, flat floodplain area near the main stem of the river, although there are some areas with steep bluffs above the channel banks. The Mississippi River channel invert ranges in elevation (within the St. Louis District) from about 430 feet at Lock and Dam 22 to about 250 feet at the confluence with the Ohio River. The typical estimated Mississippi River channel invert slope in the District is 0.5 feet per mile. Within the St. Louis District, the main tributaries are the Salt, Cuivre, Illinois, Missouri, Meramec, Kaskaskia, Big Muddy, Castor, and Cache Rivers.

Soils in the basin were predominantly deposited by the succession of continental glaciers that advanced and retreated across the area during the Great Ice Age. These sediments fall into three major categories: till, lacustrine deposits, and outwash sediments. Loess soils can also be found within the basin. In general, the soils in the basin are rich in organic matter and help explain the major land use categories: agriculture and forested areas. The climate for the basin is considered moderate and is characterized by hot summers and cool winters. The basin lies within the humid continental climate, and the area experiences four distinct seasons. Average annual rainfall is approximately 45 inches across the basin, and typically the maximum precipitation occurs in the spring (April, May, and June) and again in late November.