Because Sagamore Hill NHS is within a fragmented, suburban landscape and has experienced regular disturbance over the years, certain invasive species have significantly altered the state of some natural communities. Some of the more severely impacted areas include a patch of forest in the southwest corner of the park which has been significantly invaded by Japanese and Norway maple.

Invasives remain one of the greatest threats to the natural areas of the park, with exotic tree and shrub species (such as English ivy, wisteria, and tree of heaven) threatening the intact forest stands, and the aggressive invasive emergent Phragmites australis encroaching on the estuarine complex from developed areas to the north and south.

Invasive animal species of concern for the park include the European starling and the gypsy moth, though the latter has not been found in the park since 1996.