Current management is limited to protecting the rookery from human disturbance and conducting annual surveys to record nesting success. Plans call for removing all artificial facilities from East Marin Island, removing exotic vegetation and restoring native vegetation, supplementing nesting trees with additional native trees and establishing a protective buoy system in the tidewaters around the Islands to better protect the rookery and feeding sites from human disturbance. The refuge relies on volunteers and partners to conduct some of these activities.
Both islands consist of steep hills and sheer cliffsides and are covered in poison oak. They are closed to the public for safety purposes.
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Marin Islands NWR is managed as part of the San Francisco Bay National Wildlife Refuge Complex.