When the current bridge was planned in the 1970s, Caltrans conducted extensive environmental research on the aquatic and terrestrial environment. Principal concerns of the public were air pollution and noise pollution impacts, particularly in some residential areas of Menlo Park and East Palo Alto. Studies were conducted to procude contour maps of projected sound levels and carbon monoxide concentrations throughout the western approaches, for each alternative connection scheme}.

The local area around the bridge is an important ecological area, hosting many species of birds, fish and mammals. The endangered species California clapper rail is known to be present in the western bridge terminus area.

Near the bridge on the Peninsula are Menlo Park's Bayfront Park, East Palo Alto's Ravenswood Open Space Preserve, and Palo Alto's Baylands Nature Preserve. An accessible portion of the San Francisco Bay National Wildlife Refuge lies immediately north of the western bridge terminus, where the Ravenswood trail runs.

On both sides of the eastern terminus of the bridge are large salt ponds and levee trails belonging to the Don Edwards San Francisco Bay National Wildlife Refuge. The headquarters and visitor center for the refuge is on a hill south of the bridge approach. North of the eastern bridge terminus is Coyote Hills Regional Park, with its network of trails running over tall hills. North of that is the Alameda Creek Regional Trail, running from the Bay to Niles Canyon. East of Coyote Hills is Ardenwood Historic Farm, a restored working farm that preserves and displays turn-of-the-century farming methods