Management efforts focus on colonial nesting seabirds on off-shore islands. The refuge works with many conservation partners to provide long-term protection for seabird, wading bird, and eagle nesting islands through an active land acquisition program. Seabird restoration efforts involve predator control, monitoring, census sing, and habitat manipulation. Mainland management programs include prescribed burning and mowing on 65 acres of Refuge fields and maintaining 112 acres of wetlands in three freshwater impoundments.
Seabird islands are closed to the public during the nesting season, April 1 - August 31, to minimize disturbance to the birds. Commercial tour boats provide views of nesting seabirds on Petit Manan and Machias Seal islands.