At least 1,300 plant species have been recorded so far in the National Park, some of which are rare or endemic.
Marshes are dominated by lilies (Nymphaeaceae) (Nymphoides peltata & Nymphaea alba), iris (Iris pseudacorus), water mint (Mentha aquatica), Eurasian watermilfoil (Myriophyllum spicatum), broadleaf cattail (Typha latifolia) etc. while the arborescent vegetation mainly consists of willows (Salix spp.), poplars (Populus spp.), planes (Platanus orientalis), narrow-leaved ashes (Fraxinus angustifolia) etc. As to broadleaf evergreen and deciduous trees, there are characteristic species to be found, such as the Sessile oak (Quercus sessiliflora), the oriental hornbeam (Carpinus orientalis), the dog rose (Rosa canina), the common hazel (Corylus avellana), the sloe (Prunus spinosa), the ash (Fraxinus ornus), the small-leaved lime (Tilia cordata), the common hawthorn (Crataegus monogyna), the common ivy (Hedera helix), the maples (Acer spp.), many species of wild flowers such as orchids (Οphrys spp., Οrchis spp., etc.) crocus (Crocus spp.) etc. In the highest and coldest areas, the beech (Fagus sylvatica) is the prevailing species. These areas also host the Bulgarian fir (Abies borisii-regis), the black alder (Alnus glutinosa), the hop hornbeam (Ostrya carpinifolia), the sweet chestnut (Castanea sativa), the hawthorns (Crataegus spp.), the ash (Fraxinus ornus), maples (Acer spp.), the chequer tree (Sorbus torminalis), the common ivy (Hedera helix), the old man’s beard (Clematis vitalba), crocuses (Crocus spp.) etc.
In the wider area of Kerkini there are many endemic plant species or species that are rare both in Greece and the Balkan Peninsula. There are two endemic taxa (Asperula aristata spp. thessala, Acinos alpinus ssp. nomismophyllus), two species met only here throughout Greece (Marsilea quadrifolia, Najas gracillima) and some species rarely found in Greece (Riccia fluitans, Ricciocarpus natans, Azolla filiculoides). There are also five terrestrial species, for which Greece is the extreme limit of expansion (Crepis conyzifolia, Ornithogalum bucheanum, Peucedanum aequiradium, Peucedanum officinale, Stachys officinalis), as well as four species included in the IUCN Red List of European threatened plants (Minuartia saxifraga (R), Salvinia natans (E), Trapa natans (V), Viola stojanowii (R)).
Moreover, based on the Presidential Decree no. 67/81 on the protection of flora and wildlife, as well as on the determination of the procedure for the coordination and control of their study (GOG 23 A/30.1.1981), 11 species are found and set under protection (Atropa bella-donna, Convolvulus boissieri ssp. parnassicus, Dactylorhiza incarnata, Dianthus petraeus ssp. orgelicus, Gentiana verna ssp. balcanica, Himantoglossum hircinum, Jovibarba heuffelii, Lilium carniolicum ssp. albanicum, Lilium martagon, Orchis pallens, Viola tricolor ssp. Macedonica). Finally, 18 species are endemic species of the Balkan Peninsula (Alchemilla lanuginosa, Asperula aristata ssp. condensata, Brucuenthalia spiculifolia, Centaurea napulifera ssp. napulifera, Cerastium decalvans, Cirsium appendiculatum, Erysimum drenowskii, Galium hellenicum, Genista tinctoria, Knautia macedonica, Pedicularis brachyodonta ssp. moesiaca Scrophularia aestivalis, Silene asterias, Silene balcanica, Silene waldsteinii, Stachys plumosa, Thymus degenii, Veronica barrelieri).