The more typical black tar-and-asphalt building rooftop leads to a phenomenon called the “Urban Heat Island” effect. The endless swath of black rooftops and pavement trap heat, causing cities to be 6 to 10 degrees warmer than outlying greenbelt areas. One-sixth of all electricity consumed in the U.S. goes to cool buildings. The Academy's green rooftop keeps the building's interior an average of 10 degrees cooler than a standard roof would. The plants also transform carbon dioxide into oxygen, capture rainwater, and reduce energy needs for heating and cooling.

An open-air observation terrace enables visitors to get a close-up look at the roof's lush canopy of plants. The view encompasses the densest concentration of native wildflowers in San Francisco. The expansive vista is also an ideal location for watching Northern California’s birds, butterflies and insects. Skylights above the larger domes open and close throughout the day, enabling sunlight to reach the exhibits below. The steep slopes of the rooftop's hills draw cool air into the open piazza at the center of the building. Weather stations on the roof monitor wind, rain, and changes in temperature to help inform the automated passive ventilation systems.