On account of the distinctiveness of its geomorphology, its flora and fauna, the prefecture of Hania has a remarkably great number of rare native wildlife and plants. Major areas have been submitted under the protection of European and Greek environmental laws.

The European program "NATURA 2000", which among other things, includes major restrictions of residential and financial activities, has incorporated in its efforts the areas of:

• The lagoon of Agias next to Hania, at the outskirts of the district of Platania to the east.
• 

  Kournas Lake
  The natural lake of Kourna on the 40 th kilometer (25 th mile), en route to Rethimno.
• The isles of Gavdos and Gavdopoula, at the extreme end of the European continent, dipping into the Mediterranean, 24 nautical miles from the country off Sfakia, into the Libyan or else South Cretan Sea.
• The region of Elafonisi, 75 kilometers (46 miles) south of Hania, also on the coast that overlooks the Libyan sea. A rare biotope, with a breathtaking landscape and a unique in all Europe vegetation of native cedar trees.