Monocacy’s forests are an integral part of the park’s ecosystem. They create essential habitat for wildlife, they act as a buffer zone for delicate streams, and the native plant species that make up the forests add to the natural landscape. The different forest communities are classified as mixed oak forests, beech-maple forests, edge-type forests, and riparian zone forests.

An invasive tree known as Ailanthus altissima, or commonly referred to as Tree of Heaven, is a species of great concern for the staff at Monocacy. This tree grows very rapidly and has an outstanding ecological tolerance, meaning that it can out-compete almost all of the surrounding vegetation. When this species becomes established in an area, it will almost always out-compete surrounding native species such as oak, maple, birch and hickory. It accomplishes this through allelopathy which is a chemical process that a plant uses to keep other plants from growing too close to it. Ailanthus releases a chemical into the soil through its roots which is absorbed by nearby plants. This chemical damages the competing plant which gives Ailanthus an advantage and allows it to take over an entire area.

Finally, through the Monocacy historic tree survey, "witness trees" or trees that were present at the time of the battle, are located, marked and their data recorded. Park resource management staff record the tree species, the diameter and height of the tree, and take note of general appearance and health. GPS (Global Positioning System) technology is also being used to mark the trees' exact locations within the park allowing park staff to periodically visit the trees to assess their condition.