Wells Harbor is actually on the Webhannet River, which flows through a tidal salt marsh and in to the ocean between Drakes Island Beach to the north, and Wells beach to the south. The lower part of the river is a navigable channel, and a working waterfront, so make sure you stay close to shore and out of the channel, and keep your eyes out for boats. Once past the Harbor, feel free to paddle anywhere in the river.
There are 2 launch sites is this area. One is in the town parking lot at the northern end of Atlantic Avenue, on Wells Beach. You must pay the parking fee to the attendant to use this launch. The easiest place to launch kayaks is at the northwestern corner of the lot, where you will launch in to the lower part of the Webhannet River.
There is another launch on the western side of the river, on Harbor Road. When you drive down harbor Road from Route 1, turn right on to the dirt road just after the marsh. Past the Gazebo and to the left, there is a parking area right on the water with a small observation deck. Parking here is free, and launching is easy off the small beach. Beware that the Webhannet River is tidal, and sandbars and mudflats are exposed during lower stages of the tide (about 3 hours either side of high tide). If you're paddling up river, keep in mind that the current will flow up between low and high tide, and back down river between high and low tide. The best time to paddle up river, is when high tide is in the middle of your trip.