When you ask most local folks why the Spanish sailed past and missed discovering San Francisco Bay for over 200 years, they usually say it must have been the fog. Wrong. In 1565 it was found by heading north from the Philippines the Manila galleons could catch favorable eastern trade winds that whipped the ships relatively quickly across the broad expanse of the Pacific. They reached the west coast of North America around modern-day Cape Mendocino. Great! Then the cargo ships could sail south easily along the California coast all the way to Acapulco.
There was however a major navigational hazard along the way: the Farallon Islands. These captains were merchants, not explorers, so in order to clearly avoid smashing into those jagged, dangerous rocks there was a standard operating procedure for all galleons. When southbound and the Point of the Kings was seen -- that is the Pt. Reyes peninsula, which juts way out into the Pacific -- all vessels were to swing far, far to the west to avoid Los Farallones de los Frialles.
Therefore, fog or no fog, they were always 30 miles or more offshore, thereby unable to see the greatest natural harbor along the entire western coast of North America.
The Bay was finally discovered but not from the ocean, but from the land. Gaspar de Portola was heading from San Diego toward the capital of Alta California, Monterey, when his local guide missed the left turn along the Salinas River thereby passing that important military outpost. The party continued north until they reached the summit of 1,200-foot high Sweeney Ridge above Pacifica, where they are acknowledged to be the first Europeans to see San Francisco Bay. I always presumed Portola said something like, "Wow! This ain't Monterey, but it sure is good." The year was 1769.
This is Michael Ellis, with a Perspective.