The Ships That Lurk Below Our Feet
Much more ship discovery on FoundSF.
By the summer of 1850, over 500 vessels were recorded as being anchored in the vicinity of Yerba Buena Cove. After they had arrived, whole crews abandoned their ships, along with the passengers, to make their way up to the gold fields. Many of the vessels were eventually left to rot, others were eventually used for such purposes as storeships, saloons, hotels, jails, and some were sunk purposefully to secure water lot titles (property that was originally underwater). As wood was scarce at the time, due to the many fires that swept the city and the increasing need for building material, many of the vessels were also broken up for their timber as well as other parts such as the metal plating.
By 1851, the wharves had extended out into the cove and numerous buildings had been erected on piles near them. Over the next two decades, under various waterfront extension bills, Yerba Buena Cove was filled with sand from the downtown area. According to Bancroft, a local historian, “As late as Jan ’57 old hulks still obstructed the harbor while others had been overtaken by the bayward march of the city front and formed basements or cellars to tenements built on their decks. Even now  remains of the vessels are found under the filled foundations of houses.” The cove was eventually enclosed by a seawall which was built from 1867 to 1869, and which followed roughly along the same path as The Embarcadero.
There’s even a list of ships that were abandoned, some with great details:
Almandralina — lay near Pacific Wharf; “…on the corner of Pacific and Front, was owned at the time by M. R. Roberts…Venard’s brick building to-day covers the site where she was cut out.”  “The vessels lying at the corner of Pacific and Front streets are the remains of the ship Almandrilina — signifying almond grove — and the brig Ricardo. These vessels were owned by Captain M. R. Roberts, and were brought around the Horn early in ’49, with full cargoes for the gold fields. The captain’s young wife followed him in 1850, by way of the Isthmus, and Captain Roberts fitted-up the Almandrilina for her reception, until he completed the building of his handsome residence—at that time the finest in town—corner of Washington and Stockton streets, where they have resided every since, and where their children were born. The vessels were then converted into warehouses, and finally into boarding and lodging houses until the city front was filled in and buildings erected on top of the hulls as they lay covered up.” [FM] “Venard, G., manufacturer…625-627 Front”
For reference, here’s the 1859 Coast Survey map, with wharf names:
And you can see a sketch of the Greenwich and Lombard wharfs at the Year of the Bay exhibit at the California Historical Society.