The first buildings were erected in the 18th century by the owner of Vana-Virtsu Manor, Carl Thure von Helwig.

He designed Puhtu as a private resort with three Chinese-style houses and alleys surrounded by hewn sculptures.

In 1934 Jakob von Uexküll invited Count Alexander Keyserlingk, an amateur ornithologist, to be the guardian of Puhtu; he lived there until 1939.

After World War II, Puhtu was given to Tartu State University and shortly after that to Estonian Academy of Sciences.

Since 1995 Puhtu has belonged to Matsalu National Park, and since 1997 the station has operated as part of Estonian University of Life Sciences.