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In 1888 the South Bay Yachting Association was formed. Initially the club did not have a clubhouse and met in the back room of Samual E. "Shirt-tail" Smiths Haberdashery in San Jose at 10 South First Street - now the Bank of America building. In 1896 the club was reformed as the South Bay Yacht Club.

"During this time, pressure mounted in the south bay to realign the Guadalupe River and connect it to the Alviso Slough, which also has been know as Steamboat Slough. This was accomplished to facilitate shipping as the Port of Alviso was a major shipping point for goods going to San Francisco and the Sacramento Delta Regions. This feat was accomplished with horses, Madison scrapers and men. Leaving the Guadalupe River and Alviso Sloughs connected as they are today."
Clarence R. Boncher,
South Bay yacht Club Past Commodore and Historian

The clubhouse was built in 1903. The San Francisco Chronicle described it thusly, "The clubhouse, while simple in its appointments, will be the equal of any around the bay." The clubhouse was moved to its current "on-levee" position in 1983 because of continued flooding due to land subsidence. At that time it was graced with a coat of blue paint and called by some "The Blue Lady."

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