The Jockey Hollow and New Jersey Brigade Units of the park are largely located within the upper reaches of the Great Swamp Watershed (a sub unit of the Upper Passaic River Basin).
The park protects the headwaters of the Primrose Brook as its feeder springs surface within the park. The headwaters of the Jersey Brook are also located within the park's boundaries.
Portions of Indian Grave Brook and the Upper Passaic River traverse the park and are designated as "Wild Trout Streams" by the State of New Jersey. Upon leaving the park, the waterways eventually flow into the Great Swamp National Wildlife Refuge. The swamp woodlands, hardwood ridges, cattail marshes and grasslands of Great Swamp NWR provide for diverse and extensive wildlife habitat.
It is important to monitor and maintain water quality within the park as many of the other feeder streams into the Great Swamp have been degraded. Park staff conduct a water quality monitoring program at eleven locations within Morristown National Historical Park.