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 Main Stem Susquehanna River Watershed combines what is commonly referred to as the Middle and Lower Susquehanna watersheds and is located almost entirely
within the state of Pennsylvania with a small southern portion extending into Maryland. Elevations within the Main Stem Susquehanna River Basin study area range from 2,700 feet above sea level in the northern portion of the watershed to about 220 feet above sea level just downstream of the Marietta stream gage on the Susquehanna River.

In the northern portion of the watershed, the Susquehanna River flows southeast through steep-sided valleys separated by high, flat-topped plateaus. The Susquehanna River then confluences with the Lackawanna River flowing south through Sunbury, PA and on through the middle portion of the watershed characterized by northeast-southwest trending ridges and valleys. The downstream portion of
the watershed, starting along the Susquehanna River near Harrisburg, PA, is characterized by a narrow river valley.

On an average, this basin receives approximately 42 inches of rainfall annually. The average high and low temperatures in the watershed are along the lines of 63 and 44 degrees, Fahrenheit. There are three USACE reservoirs in the Main Stem Susquehanna study area: Stillwater Lake, Aylesworth Creek Lake, and York Indian Rock Dam. Stillwater Lake is located on the Lackawanna River approximately 4 miles upstream of Forest City, PA and 30 miles upstream of Scranton, PA. The primary purpose of Stillwater Lake is to reduce flood damages on the Lackawanna River and Main Stem Susquehanna River to the confluence of West Branch Susquehanna River at Sunbury, PA. A secondary purpose is water supply. Aylesworth Creek Lake is located on Aylesworth Creek approximately 1 mile from the confluence with the Lackawanna River in Jermyn, PA. The purposes of this project are flood risk reduction and water quality.

York Indian Rock Dam is located on Codorus Creek 700 feet upstream of its confluence with South Branch Codorus Creek. It is located about 2.5 miles upstream of York, PA. The primary purpose of York Indian Rock Dam is to reduce flood damages along Codorus Creek downstream of the dam and, to the maximum possible extent, along the Susquehanna River downstream of Marietta. The Main Stem Susquehanna River study area land use is largely characterized by forest land (47% of the watershed area) and agricultural land (36% of the watershed area). Approximately 15% of the basin area is considered urban developed and 2% of the area is considered wetland.