During the 1920s the Bayside Yacht Club had a membership roster of over 230 members hailing from all parts of Queens and Long Island. It had a fleet of over 90 boats of many types including steam yachts, schooners, sloops, and rowboats. Sailing and motor races took place throughout the season and the club awarded trophies during their annual dinners. Other social events that took place included informal dances, bridge tournaments, clambakes, holiday and gala parties, wedding receptions as well as "smokers" which were given once a month for men only. The women's activities committee included hosting annual luncheons and fashion shows.

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​By the 1930s Robert Moses and the City of New York began construction of the Cross Island Parkway and all property owners, including the Bayside Yacht Club, lost direct access to the beach and their private pier including riparian rights. The City did, however, build a bridge over the parkway at 28th Avenue to a new pier and launching facility which the Club had to share with the public.

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With low membership and a high operating budget, the Club began to fail in recent decades and the by-laws were amended in an attempt to restructure the finances. By April 1993 the Bayside Yacht Club filed for Chapter 11 bankruptcy and efforts by the Ad-Hoc Committee to Save the Bayside Yacht Club to draft a satisfactory reorganization failed.

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The Bayside Yacht Club was eventually sold to the Grace Presbyterian Korean Church in 1994 for 1.45 million dollars.