The park consists of 21 islands plus many smaller islets, 2 mainland properties and a visitor centre at Mallorytown, Ontario on the mainland. It is one of Canada's smallest national park with a total area of 9 square kilometres (3.5 sq mi).
Much of the park is only accessible by boat. Trail systems can be found on the mainland along the 1000 Islands Parkway at Mallorytown Landing, Jones Creek and Landon Bay. There are picnic, camping and oTENTik facilities on several islands and at Mallorytown Landing. Mallorytown Landing is a day use area that offers a large parking, a boat ramp, several oTENTiks, picnic gazebos, play ground, animal exhibits, travelling exhibits, and interpreters to help you along the way.
The first inhabitants of the park area are thought to have been hunting and fishing peoples who arrived following the last glacial period approximately 10,000 years ago. Many artifacts have been found in the park, including a 2500-year-old pot that was found by a diver in 1979. Pictographs are still visible on some shoreline cliffs despite damage due to acid rain and vandals.
By the early 17th century, the Iroquois people had put up large summer encampments on the riverbanks from which they fished the rich waters. Around this time they began to be visited by French explorers, fur traders, and missionaries following the St Lawrence river to seek their fortune in the new world. Following the American Revolution at the end of the 18th century, European settlers began moving into the area and the traditional fishing encampments were displaced. A few Iroquois still returned to fish, but by the 1860s fish stocks were greatly depleted.
During the War of 1812, the area of today's National Park was visited by both British and American warships. A British gunboat was sunk nearby and the preserved hull was raised in 1967. It now resides at the park. Martello towers were built in the area to defend the British from American invasion. Inside the park, Cedar Island, a small island visible from downtown Kingston, Ontario, is the site of a Martello tower named Cathcart Tower.
The park was established in 1904, the first Canadian national park east of the Rocky Mountains. It was called St. Lawrence Islands National Park until 2013, when it was renamed to Thousand Islands National Park to reflect the natural area in the name.