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The name "San Juan" was given to the San Juan Islands by the Spanish explorer Francisco de Eliza, who charted the islands in 1791, naming them Isla y Archiepelago de San Juan. The expedition sailed under the authority of the Viceroy of Mexico, Juan Vicente de Güemes Padilla Horcasitas y Aguayo, 2nd Count of Revillagigedo and Eliza named several places for him, including the San Juan Islands and Orcas Island (short for "Horcasitas"). San Juan Island itself was first discovered (by a European) by one of the officers under Eliza's command, Gonzalo López de Haro (for whom Haro Strait is named). The Spanish had found the islands a year earlier during the exploring voyage of Manuel Quimper on the Princesa Real, but it was not clear that they were islands.
Subsequent explorations of the region by the British, under George Vancouver, and the Americans, under Charles Wilkes, resulted in many of the Spanish names being replaced with English ones.
Vancouver's expedition occurred within a year of Eliza's, and Vancouver encountered other Spanish ships and traded information. Thus Vancouver knew of the names given by Eliza's expedition and tended to keep them, although he renamed some things, like the Strait of Georgia.
excerpt from Wikipedia