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 maximum water level change for Lake Winnebago is about 1.5 ft from winter pool to summer pool. During the summer months, there is only a 0.30 ft operating band that is easily surpassed if heavy thunderstorms move over the lake. The area upstream of Lake Winnebago is quite flat and marshy with several smaller shallow lakes that attenuate the flow. Improved modeling techniques in the CWMS suite of models will improve the peak flow time and volume of water into Lake Winnebago.

The Corps is authorized to regulate outflows from Lake Winnebago for flood capacity. The drawdow provides capacity to contain spring flooding, but the District does not have a tool available to quantify snowmelt. Improving the HMS model to incorporate snowmelt will benefit the District and stakeholders. In past years, the spring water level targets have been surpassed due to rapid snowmelt from rain events. While the primary authorization for regulation is to prevent flooding, the Corps also recognizes other stakeholders such as hydropower, recreational boating, fish, wildlife and wetland habitat concerns. There is a constant balance between all stakeholders.