Winchester Bay is located at 43°40'37" North, 124°10'24" West (43.677222, -124.173611).
According to the United States Census Bureau, the city has a total area of 3.65 mi2 (9.45 km2). 2.66 mi2 (6.88 km2) of it is land and 0.99 mi2 (2.56 km2) of it is covered by water. The total area is 27.12% water.
Winchester Bay is located in the Pacific Standard Time (PST) timezone, GMT-08:00. It observes Daylight Saving Time (DST).