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 Juniata River Watershed is located entirely within the state of Pennsylvania. The watershed is predominately rural, characterized by a heavily wooded, hilly terrain. Elevations within the Juniata River Basin range from 3,000 feet above sea level in the Allegheny Mountains to about 340 feet above sea level at the Juniata River’s confluence with the Susquehanna River.
On an average, this basin receives approximately 41 inches of rainfall annually. The average annual snowfall is about 25 inches. The average high and low temperatures in the watershed are along the lines of 84 and 20 degrees, Fahrenheit.

The Juniata River extends from its headwaters on the eastern slopes of the Allegheny Front, part of the Continental Divide, through the Ridge and Valley Province for 150 miles eventually draining into the Susquehanna River. The three main tributaries to the Juniata River are the Little Juniata, Frankstown Branch Juniata, and Raystown Branch Juniata Rivers.
The key streamgages in the Juniata River watershed include Juniata River at Huntingdon PA (USGS 01559000), Raystown Branch Juniata River Below Raystown Dam near Huntingdon PA (USGS 01563200), Kishacoquillas Creek at Reedsville PA (USGS 01565000), Tuscarora Creek near Port Royal PA (USGS 01566000), Juniata River at Mapleton Depot PA (USGS 01563500), Juniata River at Lewistown PA (USGS 01564895), and Juniata River at Newport PA (USGS 01567000).

Raystown Dam is the only USACE dam located within the Juniata River Watershed. It is located on the Raystown Branch Juniata River approximately 5.5 miles upstream of the confluence with the Juniata River and 97 miles upstream of the confluence of the Juniata and Susquehanna Rivers. The primary purpose of Raystown Dam is to provide flood control downstream. The dam’s secondary purposes include water quality control and low flow augmentation for warm weather fisheries, recreation, and non-Federal hydropower.

The Juniata River basin land use is largely characterized by forest land (70% of the watershed area) and agricultural land (20% of the watershed area). Approximately 1% of the basin area is considered urban developed.