Honeoye Lake is one of a group of long and narrow lakes located in western New York State known as the Finger Lakes. The basins of these north-south oriented lakes were formed by the advance of ice masses during the Ice Ages, and further sculpted by glacial meltwater during the interglacial and postglacial periods. Although the lake posesses the long and narrow shape characteristic of the Finger Lakes, it is by far the shallowest (4.9 m) of the group. In addition, it is comparatively small (7.05 km2), has the shortest retention time (0.8 yr) and is generally the warmest. As might be expected from this description, Honeoye Lake is considered one of the most eutrophic of the Finger Lakes. Although the Finger Lakes region is now well-known for its many vineyards and orchards, it had been densely forested up until the early 1800's when large areas were cleared for agriculture by white settlers. The forests are now in the process of expanding as marginal farmland is abandoned and gradually invaded by trees.

Of Honeoye Lake's 95 km2 drainage basin, approximately 85% is forested (the highest proportion among the Finger Lakes), 10% is actively farmed, and 2% is residential. The lake is used extensively for recreation, including swimming, boating and fishing. Lakefront property is privately owned, and highly developed. As a result, water quality has suffered from failing septic systems, oil from power boats, and other causes. The climate of Honeoye Lake is characterized by cold, snowy winters and warm, dry summers; and the lake regularly freezes over in the winter.