In Classical times, the Prespa region formed part of ancient Lýnkos (Λύγκος), and the lakes were called Little and Great Brygeis.
In the 10th century, the Tsar Samuil built the fortress and church of St. Achillius on an island called Agios Achillios in the Small Prespa Lake, on the Greek side of the border.
The biggest island in the Great Prespa Lake, within North Macedonia, is called Golem Grad ("Large Town"), and Snake Island (Zmiski Ostrov).
The other island Mal Grad ("Small Town", in Albania) is the site of a ruined 14th century monastery dedicated to St. Peter.
Today, both islands are uninhabited.

Because Great Prespa Lake sits in limestone country about 150m above Lake Ohrid, which lies only about 10 km (6.21 mi) (6 miles) to the west, the only outlets for its waters are through underground channels in the karst and emerge from springs which feed streams running into Lake Ohrid.

For many years, the Greek part of the Prespa Lakes region was an underpopulated, military sensitive area which required special permission for outsiders to visit.
It saw fierce fighting during the Greek Civil War and much of the local population subsequently emigrated to escape endemic poverty and political strife.
The region remained little developed until the 1970s, when it began to be promoted as a tourist destination.
With an abundance of rare fauna and flora, the area was declared a Transnational Park in 2000.
 In 1999 the Society for the Protection of Prespa received the Ramsar Wetland Conservation Award for its conservation efforts regarding the Lake Prespa Ramsar site, and was eventually included on 3 July 2013.

In 2018, Great Prespa Lake was the setting for the signing of the Prespa Agreement, intended to resolve the Macedonia naming dispute by renaming the Republic of Macedonia to North Macedonia.
 The agreement was signed on 17 June 2018 in a high-level ceremony at the Greek border village of Psarades on the lake, by the two foreign ministers Nikola Dimitrov (of the Republic of Macedonia) and Nikos Kotzias (of Greece) and in the presence of the respective prime ministers, Zoran Zaev and Alexis Tsipras.
After the ceremony, Tsipras and Zaev crossed over the border to North Macedonia's side of the lake for lunch at the village of Oteševo, in a highly symbolic move that marked the first time a Greek Prime Minister ever entered the Republic of Macedonia since it declared independence in 1991.
In Classical times, the Prespa region formed part of ancient Lýnkos (Λύγκος), and the lakes were called Little and Great Brygeis. In the 10th century, the Tsar Samuil built the fortress and church of St. Achillius on an island called Agios Achillios in the Small Prespa Lake, on the Greek side of the border. The biggest island in the Great Prespa Lake, within North Macedonia, is called Golem Grad ("Large Town"), and Snake Island (Zmiski Ostrov). The other island Mal Grad ("Small Town", in Albania) is the site of a ruined 14th century monastery dedicated to St. Peter. Today, both islands are uninhabited.
Because Great Prespa Lake sits in limestone country about 150m above Lake Ohrid, which lies only about 10 km (6.21 mi) (6 miles) to the west, the only outlets for its waters are through underground channels in the karst and emerge from springs which feed streams running into Lake Ohrid.
For many years, the Greek part of the Prespa Lakes region was an underpopulated, military sensitive area which required special permission for outsiders to visit. It saw fierce fighting during the Greek Civil War and much of the local population subsequently emigrated to escape endemic poverty and political strife. The region remained little developed until the 1970s, when it began to be promoted as a tourist destination. With an abundance of rare fauna and flora, the area was declared a Transnational Park in 2000.  In 1999 the Society for the Protection of Prespa received the Ramsar Wetland Conservation Award for its conservation efforts regarding the Lake Prespa Ramsar site, and was eventually included on 3 July 2013.
In 2018, Great Prespa Lake was the setting for the signing of the Prespa Agreement, intended to resolve the Macedonia naming dispute by renaming the Republic of Macedonia to North Macedonia.  The agreement was signed on 17 June 2018 in a high-level ceremony at the Greek border village of Psarades on the lake, by the two foreign ministers Nikola Dimitrov (of the Republic of Macedonia) and Nikos Kotzias (of Greece) and in the presence of the respective prime ministers, Zoran Zaev and Alexis Tsipras. After the ceremony, Tsipras and Zaev crossed over the border to North Macedonia's side of the lake for lunch at the village of Oteševo, in a highly symbolic move that marked the first time a Greek Prime Minister ever entered the Republic of Macedonia since it declared independence in 1991.
Lake Prespa