Construction began in May 2006 on the Bridge North Approach Physical Security Improvements Project. The security enhancements include new gates, fencing and lighting, as well as the installation of automated vehicle barriers and new equipment such as sensors and cameras. Construction was completed in 2006. It is anticipated that construction of the South Approach Physical Security Improvements Project will commence in late 2007. The improvements contemplated for the South Approach are similar to the improvements constructed at the North Approach.

Doyle Drive, located within the Presidio of San Francisco, winds 1.5 miles along the northern edge of San Francisco Bay and connects to the San Francisco peninsula to the Golden Gate Bridge and the North Bay. Originally built in 1936 with narrow lanes, no median, and no shoulder, Doyle Drive is approaching the end of its useful life. Currently it is used by nearly 120,000 vehicles every weekday.

The Doyle Drive Project considered several alternatives to improve the seismic, structural, and traffic safety of Doyle Drive within the setting and context of the Presidio of San Francisco and its purpose as a National Park. The Draft EIS/R Section 4(f) Evaluation was released on December 30, 2005 and considered a No Build Alternative, Replace and Widen Alternative, and Presidio Parkway Alternative.

Over 800 comments were received following the public circulation period of the DEIS/R, with over 300 comments on the project alternatives, of which more than 150 comments expressed a preference.  Based on consultation with agencies, interested parties, and the citizen's advisory group, the San Francisco County Transportation Authority Board selected the Presidio Parkway as the Preferred Alternative to be identified in the Final Environmental Impact Report. The Presidio Parkway design replaces the existing structures with a new parkway-type roadway that includes short tunnels, new access, and improved views from within the Presidio. Final action on the project is expected to occur in 2007.

Following the transfer of Fort Baker from the Army to the National Park Service, a reuse concept was developed that included a conference and retreat center at Fort Baker, which will include programs furthering the NPS mission to conserve natural and historic resources and provide for their public enjoyment. NPS has recently contracted with a San Francisco development firm to create the retreat and conference center called "Cavallo Point" that will have 142 rooms with an average size of 600 square feet. The centerpiece of the project is the Fort Baker Institute, which will host lectures and provide a forum for environmentalists, researchers and policymakers to address environmental issues. The homes and other buildings that ring Fort Baker's 10-acre parade ground will be restored, and an 8,000 square foot healing arts center and medicinal herb garden will be built. Cars will largely banished and guests urged to walk, ride bikes or take a shuttle.

The Fort Baker Plan also includes creating a waterfront park that will provide panoramic views of the Bridge, San Francisco Bay, San Francisco skyline, and Alcatraz. Under the proposed plan, Fort Baker's waterfront and other open space will be transformed to create a multitude of opportunties for visitors to enjoy the area's scenic beauty, a hike, bike, sail, kayak, picnic, and explore. The U.S. Coast Guard Station will remain at Fort Baker.