- Koufonissia are located within the narrow strait between the islands of Naxos and Amorgos. They constitute a cluster of three small islands (Kato Koufonissi, Keros, Pano Koufonissi) as well as nine islets.
- The climate is temperate-Mediterranean with stormy winds during winter and rather warm dry summer periods. The average temperature is ranging between 11ο C and 25ο C. There are winds blowing all year long in north-eastern directions, whereas the waves formed at the passage between Koufonissia and Naxos reach up to 4m long.
- The geological composition of the islands (transitions of marly limestone and sandstone) in combination with a few rainfalls and the absence of watersheds because of their small area, constitute the main factors that render fresh water rather insufficient.
- Weather conditions and the absence of fresh water deposits have not favoured the agricultural development which is limited to barley cultivation for manufacturing animal feed.
Livestock farming, instead, is developed and it mainly involves the breeding of sheep and goats as well as cattle. There are free range animals, most of which live in Keros (7,000 sheep and goats), whereas some flocks are browsing in Kato Koufonissi.
- The islands and islets of the area are very important to the immigrant birds as well as to some rare/endemic plants such as: Colchicum cousturieri, Arenaria aegea (Antikeros), Nigella degenii (Kato Koufonissi), Fibigia lunaroides (Antikeros), Anthemis scopulorum (Antikeros), Allium luteolum (Keros, Antikeros).
- In the wider marine area, Posidonia meadow fields are cultivated. The Monachus monachus seal finds shelter in various spots. A couple of other significant species of sea mammals that have been identified in the area are the Delphinus delphis dolphins and the Phocaena phocoena cetaceans.
- Regarding the terrestrial fauna, the endemic subspecies of the Podarcis erhardii
amorgensis lizard has been traced in Pano Koufonissi and Keros.
- Until the end of 20th century, fishery was the inhabitants' exclusive activity. Today there are 60 commercial fishing vessels in Pano Koufonissi, which provide their fish to the market of Naxos and the fish market of Piraeus via the Volakas port. Inhabitants usually jest about their vessels being more than the number of the families who live in the island.
In the past few years, since Koufonissia have been rated as a top destination of alternative tourism in Cyclades, a great number of inhabitants started running tourist businesses.
The entire island cluster of Koufonissia is part of the European network of protected areas NATURA 2000.