The San Andreas fault line is the geologic fault between the Pacific plate and the North-American plate at the level of San Andreas. The fault line goes through the San Fierro Bay, and under the Gant Bridge. Because of the fact that San Fierro is so close to the fault line, the city had to suffer some major earthquakes. In 1988 an earthquake destroyed several blocks of houses in Doherty and a double deck motorway next to the Garver Bridge collapsed.
The San Andreas fault line is a reference of the fault line in San Francisco with the same name (note that the fault line in the game never is mentioned by name, but that it's name is given by fans). Also San Francisco had to suffer several major earthquakes.
The real San Andreas fault line for that matter looks like a long ridge at the bottom of the ocean, and not like a trench, like in GTA San Andreas. Also the real fault line goes parallel along the coast-line, in stead of through the bay.