The Antique Boat Museum is a non-profit educational facility located on Mary Street. The museum displays hundreds of antique boats and river artifacts and offers classes for both children and adults. It also provides tours, boat rides and cruises. The museum was established in the early 1970's and currently has approximately 2200 members internationally. The Museum sponsors an annual Antique Boat Show which attracts over 10,000 people per year. A popular event during the Show is the boat auction. The museum also sponsors a Race Boat Regatta every two years. The most recent addition to the museum is the skiff livery, a display of non-motorized antique boats.

The Handweaving Museum & Arts Center are located on John Street and was established in 1964. The primary goal of the organization is to promote arts and crafts through education, research, exhibits and programs. The Craft School programs are available to everyone and include specialized programs such as after school art programs, Elder hostel programs and conferences for weavers. The organization also hosts family events and sponsors the annual Antique Show and Craft Show. The School/Museum has 300 members and employs a full time administrator, curator, housekeeper, and Green Thumb worker.

The Thousand Islands Museum is a non-profit educational facility. It was established in 1964 and is located in the Town Hall on Riverside Drive. It is an educational facility with a collection of preserved artifacts from the St. Lawrence River, Clayton, and the Thousand Islands region. The museum is known as a "turn of the century" historical museum because it has collections of artifacts from the early 1900's.

The museum is staffed by one part-time and one full-time employee, a governing Board of Trustees and approximately twenty volunteers. It sponsors the annual Clayton Decoy Show, both held at the Clayton Recreation Arena. They often sponsor live performances and model boat shows. There is an ongoing program called "History at Noon" and two new exhibits, the pictorial wall and a Native American exhibit.