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Geologically the inlet is a fjord carved by the retreat of the glaciers during the last ice age approximately 13,000 years ago.
The Quinnipiac River empties into the inlet on its north end.
The harbor is protected from Long Island Sound by a peninsula from its western side, once known as "Little Necke" but now called Lighthouse Point, because of the lighthouse that was constructed on its tip in 1805. The original lighthouse was replaced in 1845 by the current structure, called the New Haven Harbor Lighthouse .
In July 1779, the peninsula was the scene of an amphibious landing by British troops