Puhtulaid was inhabited in the middle of the 18th century, when a local landowner, Carl Thure von Helwig, who was a district executive, established a summer resort here and redesigned the deciduous forest into a Dutch garden. A so-called Chinese house and many smaller houses and pavilions were built on the islet. The landowner Von Helwig was also an eager stonemason, who made tens of monuments for the important people in his family. Some of these monuments have survived and have been gathered to a small valley in the southern point of the peninsula. The most famous and oldest of them is the monument dedicated to the famous poet Friedrich Schiller. Dorothea, the daughter of Carl Thure put up the monument because she was friends with Charlotte, the wife of the poet. The original pieces of the monument are currently in the museum of Haapsalu Old Town Hall. A copy of the monument that differs slightly from the original was made by Paul Horma and can be found at the park in Puhtu.
In the second half of the 19th century, the baroness of Virtsu, Elisabeth von Uexküll redesigned Puhtu into an English-style park – straight roads were replaced with more natural ones, stands and bushes were allowed to grow their own course. There were a Family House, a building for eating, some little one-family houses and pavilions at the different parts of the Puhtu park. The park had 7 km of sand roads that were raked every morning. There was a pleasure garden next to the Family House and behind it a natural wooded meadow where the oldest oak trees on the island grew.
During World War I, there was a Russian air base with a jetty on the western shore of Puhtulaid for water planes. Almost all buildings, except for the cattle manor with a barn that were built in 1857, were destroyed and burnt before departure. Puhtulaid belonged to Professor Jakob von Uexküll between 1928 and 1940. He also built the summer house where Puhtu-Laelatu Biology Station currently operates in the southern point of the peninsula. In 1934, Count Alexander von Keyserlingk, an environmentalist and amateur ornithologist, was called to maintain the island. He lived in the cattle manor of Puhtu until 1939. Thereafter, Jakob von Uexküll, who was leaving Estonia, sold his property to the University of Tartu and as of 1949 until today, Puhtulaid has belonged to different research institutes.
In the middle of the 19th century, a road dam and a bridge were built on the strait, with a width of 700 m, between Virtsu and Puhtulaid. Puhtulaid has been a peninsula since 1952 when the bridge was replaced by a stone dam.