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The best way to see geological fault lines is from the air, over the middle of the state. But if an air trip is not in the cards, both Point Reyes at Bear Station and Crystal Springs Reservoir have spots where you can see fence posts that cross the fault, demonstrating how far the earth moved that day a little over a hundred years ago. You could take public transit to (near) Crystal Springs, but it may be complicated and involves a lot of walking.
At Point Reyes, there is an "earthquake walk" that is on the actual fault offering some interesting displays enroute. It includes a fence that was separated by about 6 feet when the earth slid in the 1906 quake.
Visit the outdoor exhibit just across the parking lot from the Bear Valley Headquarters and Visitors Center of the Point Reyes National Seashore. Visitors can ask the rangers or docents to point out the two different geological formations that are on either side of the San Andreas (and watch the peninsula on the west side travel northward at its 1-2" per year pace)!
Also in Marin County is the United States Army Corps of Engineers' museum in Sausalito, CA. Not only does this free-admission museum have displays regarding the 1906 San Francisco earthquake and the national disaster responses for it. But it is more famous for a massive working model of the entire San Francisco Bay water flow, commonly known to generations of Bay Area school children as "The Bay Model". It covers the area of nearly three football fields in size. Its ebbs and flows mimic the real tides in real time.
An easy thing to do is to visit UC Berkeley, via BART and walk around the stadium to see evidence of the Hayward Fault, a branch of the San Andreas Fault system. UC Berkeley's Lawrence Hall of Science has some good exhibits.
Heading south along the San Andreas Fault to San Mateo County, Crystal Springs Reservoir is a visible example of the fault. The valley runs north-south, different than most all coastal valleys, because the fault runs directly beneath it. The lateral movement has created the rift. Fault lines are normally only visible shortly after the movement. Time heals most scars. Beginning in 2005, docent led hikes of the closed areas of the Crystal Springs watershed became available. This is the only public access allowed in the closed areas.
There are some vista points near the Crystal Springs reservoir along Highway 280 (best accessed heading northbound) with lookout points from where one can easily observe many miles of the San Andreas Fault, including San Andreas Lake.
The United States Geological Survey Headquarters is in Menlo Park, CA. This is another good source of information on earthquakes in the Bay Area. It is one of the best in the world.
Heading south, at the border of the Forest of the Nicene Marks State Park in Santa Cruz County and Uvas Canyon County Park in Santa Clara County in the coastal mountain range is the epicenter of the 1989 Loma Prieta earthquake. It is accessible to hikers.
Anyone driving further south to Monterey can detour a bit from Watsonville, via Highway 152 or Highway 156, to Hollister and San Juan Bautista Mission to see the fault. The view of the scarp from the mission is impressive, especially the deformations on the streets. In Hollister, the evidence is on sidewalks and old buildings, too. And, as of Fall 2006, a new "Helicorder" (drum recorder) seismograph is now mounted in one of the Mission San Juan Bautista's museum rooms, with a long period of recorded activity on the drum... safe from the weather and vandalism that its predecessor was exposed to outside the mission church. For the backstory:
South of Monterey, near Soledad is the Pinnacles National Monument. After this ancient fault-straddling volcano blew-up, its halves separated. This western half of the volcano's remains are now about 200 miles northwest on the San Andreas fault from the other half, near Lancaster, CA. The halves continue to get farther apart.
Note: Some of the original information for this thread came from the following forum thread: