According to the United States Census Bureau, the Wauregan CDP has a total area of , of which , or 1.25%, are water. The CDP includes, in addition to the original village, the village of West Wauregan across the Quinebaug River in the town of Brooklyn, as well as tracts of open land to the north, newer residential development to the south, and modern commercial properties along Route 12.
According to the United States Census Bureau the Wauregan CDP has a total area of  of which  or 125% are water The CDP includes in addition to the original village the village of West Wauregan across the Quinebaug River in the town of Brooklyn as well as tracts of open land to the north newer residential development to the south and modern commercial properties along Route 12