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)

About 1,100 air miles north of the Gulf of Mexico at an elevation of 1,465 feet above sea level, the outlet of Lake Itaska in north central Minnesota is the origin of the Mississippi River, and the river flows almost 2,400 twisting and turning miles to the Gulf. The Mississippi River starts its journey flowing north, then east, and then in a great sweeping arc turns back to the southwest to Brainerd, Minnesota where the river begins flowing to the south and southeast. The headwaters of the Mississippi River is a region of dense forests, great swamps, and thousands of lakes. Below the Twin Cities, where the Mississippi River is joined by its largest tributary in the St. Paul District, the Minnesota River, the flow is through a valley from one to three miles wide between bluffs which are 200 to 600 feet high. A short distance below St. Paul, the Mississippi River is joined by another large tributary, the St. Croix River. Below Red Wing, Minnesota, the river enters Lake Pepin which was formed by the delta of the Chippewa River, and near the southern limit of the St. Paul District, the Wisconsin River empties into the Mississippi River.

In the St. Paul District, the Mississippi River and its tributaries drain an area of almost 80,000 square miles, of which 45,000 square miles are in Minnesota, 32,000 square miles are in Wisconsin, and the remainder are in South Dakota and Iowa. In this district, the Mississippi River drops almost 60% of its total fall. In the northwestern portion of the State of Minnesota, channels of streams have flat gradients and meander through shallow valleys. In north central Minnesota with its heavy forest cover, flat land slopes, and large storage capacity in lakes, swamps, and reservoirs, there is no serious flood problem. However, in the southeastern part of the State, the tributaries, flowing from the prairies to the main stream, have cut deep gorges through the soft limestones and sandstones which form the bedrock in this area. The relatively high rainfall, averaging up to 32 inches per year combined with the steep gradient of the channels, cause these streams to have occasional flash floods. Soil erosion, silting, large discharges, and high velocity may cause serious problems.

The portion of the watershed modeled by this effort extends from the Twin Cities (Minneapolis – St. Paul metropolitan area) to Guttenberg, IA near Lock and Dam 10. This includes the St. Croix River, Chippewa River, and Wisconsin River. Modeling of the Minnesota River is being completed under a separate CWMS basin modeling effort in FY16.