1. Oligotrophic waters in medio-European and perialpine area with amphibious vegetation, code no. 3132. It appears in those spots at the lakeshore, which in the summer season are not covered with water. Characteristic species: Cyperus fuscus, Amaranthus blitum, Rorippa sylvestris and Paspalum paspaloides.
2. Natural eutrophic lakes with plant communities of associations between Magnopotamion and Hydrocharition morsi-ranae, code no. 3150. These include all plant communities of aquatic vegetation appearing in Lake Kerkini: a) vegetation of freely-floating aquatic plants (lesser duckweed species, salvinia species, water plant species), b) vegetation with aquatic macrophytes completely under water (mesopleustophytes) and submerged macrophytes.
3. Floating vegetation of river aquatic plants, code no. 3260. In areas with little or no water flow, the species of Potamogeton nodosus is very common and accompanied by the species of Lemna minor, Cladophora sp.
4. Mediterranean rivers with constant flow (Paspalo-Agrostidion) and dense vegetation with a form of curtain by Salix and Populus alba along the banks (code: Natura 3280). This is met at the lakeshores and at Strymonas delta.
5. Alpine and sub-alpine heathlands, code no. 4060. It refers to the pastures at the top of Mount Kerkini.
6. Semi-natural xerophyte meadows on carbonate substratum, code no. 6211, which includes the grasslands and the brushes in the foothills of the mountains.
7. Mediterranean meadows of high grass and rush (Molinio – Holoschoenion), code no. 6420. It includes the surface of old beds and banks of river Strymonas.
8. Reeds under code no. 72Α0. They mainly appear along the north shoreline of the lake and in channels.
9. Silicic rocky slopes with chasmophytic vegetation, code no. 8220.
10. Beech forests of Asperulo-Fagetum plant community, code no. 9130. The specific habitat concerns the high beech forests in the mountains.
11. Canyon forests with Tilio – Acerion, code no. 9180. They were recorded in the canyon of Mount Kerkini at an altitude of 500-700 m.
12. Residual alluvial forests (Αlηion glutinosae-incanae), code no. 91Ε0, which includes the riparian (water) forests of Strymonas and the streams, mainly consisted of alders.
13. Beech forests with broadleaf oaks (Quercus frainetto), code no. 9280. These appear in the transition zone between oaks and beeches.
14. Forest halls with Salix alba (white willow) and Populus alba (white poplar), code no. 92Α0. The specific habitat includes the riparian forests of river Strymonas.
15. Forests of oriental plane woods (Platanion orientalis), code no. 92C0. The specific habitat includes the riparian plane woods of Strymonas (plane groves).
16. Beech forests of Luzulo-Fagetum plant community, code no. 9110. These are the high beech forests in the mountains.
17. Forests of oak and hornbeam of Galio-Carpinetum plant community, code no. 9170. These are on the low hills of the mountains.
18. Mixed forests of oak, elm and ash along great rivers, code no. 91F0. The specific habitat includes the riparian forests of the bed of Strymonas, which are flooded with the regular rise of the water level, or on the low hills flooded with the rise of aquifer and consist of species such as elm, ash, black poplar etc.
19. Greek beech forests with Abies borisii-regis, code no. 9270. They are mixed forests of beech and fir at the border on the east end of Kerkini Mountains.
20. Forests of upland conifers with forests of black pine trees (Pinus nigra ssp. pallasiana), code no. 9536, mainly concerning afforestations in the Mount Kerkini.
21. Chestnut forests under code no. 9260. This habitat consists of chestnut forests and is found at the border on the east end of Kerkini Mountains.
Habitats under code numbers 6211, 9180 and 91Ε0, which concern semi-natural xerophytes meadows, canyon forests with Tilio – Acerion and residual alluvial forests (Αlηion glutinosae-incanae) respectively, are habitats of priority for the E.U. and thorough work on their conservation both by the management bodies and the citizens is necessary.