Toksook Bay is located at 60°31'48" North, 165°6'7" West (60.530000, -165.102222).
According to the United States Census Bureau, the city has a total area of 74.02 mi2 (191.70 km2). 33.08 mi2 (85.67 km2) of it is land and 40.94 mi2 (106.03 km2) of it is covered by water. The total area is 55.31% water.
Toksook Bay is located in the Alaska Standard Time (Alaska ST) timezone, GMT-09:00. It observes Daylight Saving Time (DST).