The small wetlands, salt marshes and dunes of Naxos are a haven for birds, fish and reptiles. The most important wetland is that of Alyki which comprises a large lake southwest of the airport runway. It is the largest salt lake in the Cyclades and retains enough water. The vegetation includes reeds, aquatic plants and clumps of cedar trees. 166 bird species have been observed and it is enlisted in the protected areas of NATURA 2000 network.
Four wetlands of the island have been also included in the list of small island wetlands of up to 80 acres, of the Ministry of Environment. According to the Presidential Decree of 2012, the marsh in Pyrgaki, the mouth of Skoulikaria springs in Ammitis, the marsh of Agiassos and the marsh of Kalandos joined the list among 380 small wetlands and came under protection.