Flora of the national park "Vodlozersky" has pronounced boreal look. Nemoral species are presented lightly and registered mainly in environs of Lake Vodlozero.
The flora of the park contains over 500 species of vascular plants, about 150 species of leaf-caulescent and hepatic mosses, over 100 species of lichen. The majority of species are typical for taiga zone. Of them, three species are included into Russia's Red Data Book: Dactylorhiza traunsteineri (orchis), Calypso bulbosa (Pink Fairy Slipper), Lobaria pulmonaria. Here, at the utmost western boundary of their locality you can find a great deal of Eastern (Siberian) species: Larix sibirica (Siberian larch),
Rubus humulifolius (raspberry-bush), Atragene sibirica etc.Flora of park's bogs is typical or etalon for the bog's flora of taiga zone of the European north of Russia. It contains more than 200 species of vascular plants, mosses and lichens. Different species of sphagnous mosses, cotton-grass, sedges and marsh undershrubs predominate in flora.
Here grows such rare plants as Dactylorhiza traunsteineri (orchis), Epipactis palustris (helleborine), Platanthera bifolia (butterfly orchid), Gymnadenia conopsea (nigritella) etc.
Coastal and water vegetation is formed from plants which are adapted to live in shallow waters and in zones of temporary flood. Usually those are reed (Phragmites), marsh horsetail (Equisetum palustre), and sedge (Carex acuta). Common floating pondweed (Potamogeton natans), yellow water lily (Numphar lutea), white water lily (Numphaea candida) are spread in still back-waters of rivers and covered from the wind parts of lakes.