The hamlet of Honeoye was first inhabited thousands of years ago by the Point Peninsula Indians, followed by the Seneca of the Iroquois nation. During the American Revolution, American troops built a small garrison there known as Fort Cummings in order to drive the Seneca from the frontier. The Indians had allied with the British, thereby attacking American settlers living in the area. As a result, George Washington ordered the destruction of the Seneca villages, crops, and people.
After the War, some of these soldiers chose to return and resettle in western New York because of its fertile soil. In the mid-19th century, this area had numerous abolitionists, feminists, and other progressive activists. Stations of the Underground Railroad were founded in western New York to help convey escaped slaves to freedom in Canada.
Honeoye remained a largely agricultural community until the early part of the 20th century, when many wealthy people from Rochester, New York took interest in Honeoye Lake as a resort area. Its relatively shallow depth gave it warmer temperatures than the Great Lakes.