Tree mortality incurred through the nesting habits of Double-crested Cormorants (Phalacrocorax auritus) can cause human-wildlife conflicts, often resulting in the lethal control of cormorants to reduce local population numbers in North America. In a protected area in Toronto, Ontario, Canada, that supports the largest colony of Double-crested Cormorants in North America, a non-lethal management approach to mitigate cormorant-induced tree mortality was adopted by the site managers in 2008. Double-crested Cormorants were managed for space occupancy rather than population size, with the main objective of minimizing tree mortality while supporting the cormorant population. Targeted non-lethal deterrence of tree-nesting Double-crested Cormorants was labor intensive, but effective in protecting trees. Between 2008 and 2016, the tree-nesting colony was prevented from expanding. Accessing ground-nesting Double-crested Cormorants only at night to avoid Larus sp. predation of Double-crested Cormorant nests appeared to be highly effective in minimizing disturbance; the ground-nesting colony expanded 899% over an 8-year period, with a 44% decrease in tree nesting. Ground-nesting Double-crested Cormorants had less impact on trees than tree-nesting individuals, and this spatially focused approach allowed for the sustained existence of a thriving colony.