Wells Harbor is a protected cove located on the lower Maine Coast. Additionally, the Wells Harbor Inlet is the point at which the Webhannet River empties into the Atlantic Ocean.Wells Harbor is 4.5 miles southwest of Kennebunkport and 19 miles north of the New Hampshire/Maine state line.ff in the upper-left-hand (south) corner of the image, Wells Beach is visible, while off to the right (north) is Drakes Island Beach. Off in the distance at the very top of the image is the Wells Harbor town dock.