The station went on the air as WAYD in February 1999, programming an adult standards format branded as "The Bay." It was owned by Gopher Hill Communications, who also owned WQSS in Camden and WABI and WWBX in Bangor; the station was based out of the WQSS studios in Camden. On April 16, 2001, the station changed its call sign to the current WBYA, which had just been dropped by WFZX in Searsport. Gopher Hill sold WBYA to Mariner Broadcasting in 2003; this came after the other three Gopher Hill stations were sold to Clear Channel Communications. Mariner kept the standards format, but dropped locally-produced programming in favor of the Music of Your Life service.Nassau Broadcasting Partners acquired Mariner in 2004; under Nassau, the station switched to the "Frank FM" classic hits format on April 1, 2005.
WBYA, along with 16 other Nassau stations in northern New England, was purchased at bankruptcy auction by WBIN Media Company, a company controlled by Bill Binnie, on May 22, 2012. Binnie already owns WBIN-TV in Derry, New Hampshire. The deal was completed on November 30, 2012.