Dead people don't pay taxes and they take up precious real estate, so San Francisco decided in the early 20th century to evict them—or at least to find a way to hide them. This society newsletter from 1992 has the grisly timeline.
1901Walls, crypts and markers from the Laurel Hill Cemetery were dumped into the bay to become the Marina Yacht Harbor jetty—now home to a nifty Wave Organ. Thousands of displaced San Franciscans wound up in the necropolis at Colma, which was created so the city wouldn't have to trip over its dead pioneers.
The city supervisors prohibited further burials in the city limits.
City supervisors were granted permission to use Golden Gate Cemetery as a park. Mausoleums and tombstones were removed and disposed of down a convenient ravine at Land's End. Those bodies that were not removed were covered over and the area became the Lincoln Park Golf Course.
All remaining burials were ordered out of the city.
If you need help figuring out where your San Francisco ancestors were deposited, San Francisco Genealogy is a good place to start.