Nearly 400 plant species, classed as endangered in the Czech Republic, grow in the Třeboňsko PLA, of which 104 are protected (34 species are critically-endangered, 34 highly-endangered and 35 endangered). The Třeboňsko landscape is also enriched by its extensive coniferous and deciduous forest, where we can find local varieties of central European trees and shrubs. One of the most significant is the local variety of Scots pine (Pinus sylvestris) with a slim, straight trunk and branches only growing near the apex.
Another rare species is the bog-pine - Pinus rotundata, which together with Scots pine and their interspersed hybrids form a completely unique ecotype of peaty forest with the largest Czech population of labrador tea (Ledum palustre). Cow-wheat Melampyrum bohemicum grows locally in the dry, sandy pinewoods in the Třeboňsko and very occasionally we may find spring anemone (Pulsatilla vernalis) or umbellate wintergreen (Chimaphila umbellata). A wealth of flowers can be found in the remnants of deciduous stands, such as moonwort (Botrychium lunaria) and the rare branched moonwort (Botrychium matricariifolium), asarabacca (Asarum europaeum), the bedstraw Galium sylvaticum, hepatica (Hepatica nobilis) and many more. In the alluvial forests and alder stands on riverbanks and around the edges of the older ponds the rare crested shield fern (Dryopteris cristata) and water arum (Calla palustris) grow, as does the protected tufted loosestrife (Potentilla thyrsiflora) which is common here, or the water violet (Hottonia palustris).
The herb-rich meadows, peaty meadows and sedge communities of the Třeboňsko have a very rich variety of plants and harbour a large number of species which only occur at a small number of isolated localities in central Europe and are in danger of complete extinction. Three species of insect-eating sundews grow here, as well as numerous protected species such as bogbean (Menyanthes trifoliata) and marsh (Inundated) club-moss (Lycopodiella inundata). The flora of the living peatbogs, their developmental stages and transition to peaty forests is represented by an exceptionally large number of moss species. A complete range of shrubs from the heather family grow in many places, including marsh andromeda or bog rosemary (Andromeda polifolia), cranberry (Oxycoccus palustris), labrador tea and others. The Třeboňsko PLA is known for its species diversity of aquatic plants in still and flowing waters, which were predominantly dystrophic and oligotrophic in the past, but are becoming more mesotrophic and eutrophic at present. Among the rarest aquatic plants is least water lily (Nuphar pumila) which has almost disappeared, although yellow water lily (Nuphar lutea) and white water lily (Nymphaea alba) are more common. Several species of carnivorous bladderworts and two species of hornworts also grow here.
A whole range of exceptional plants occur on the periodically-exposed fishpond bottoms and on the sandy banks, including violet crystalwort (Riccia huebeneriana), bristle-seed sand spurrey (Spergularia echinosperma) and pillwort (Pilularia globulifera).
On the dry sandbanks, air-blown sands and dry forest margins in the Třeboňsko PLA, we can find xerophilous communities with the rare Shepherd’s cress (Teesdalia nudicaulis), wild thyme (Thymus serpyllum) or the fescue Festuca filiformis.