The landscape protection area can be conditionally divided into two parts: the island of Kassari and Käina Bay.

Kassari Island
Landscapes that are directly connected to human activity are a big value for the island of Kassari. As a result of the collaboration between human and nature, valuable semi-natural communities have formed: meadowlands, wooded and coastal meadows.

Coastal meadows are levelled and shallow stretches on the beach that are usually either grazed or mowed. A big part of the coastal meadow is regularly flooded with sea water. There are patches of salinas also at places in the meadows where halophilic plants, i.e. the common glasswort (Salicornia europaea), find a habitat. The pedunculate sea-purslane (Halimione pedunculata) also feels comfortable on the coastal meadows here. Coastal meadows are an important site for the nesting and peregrine birds of the protection area.

The mosaicism of the landscape is characteristic to the wooded meadow where small hayfields alternate with groves. Meadow as well as forest biota can be found in the wooded meadow because of the different light and humidity conditions. The plant communities of the wooded meadow have the highest biodiversity in the world.

Alvars have formed on limestone areas with a thin layer of soil. Plants that are lime-loving and tolerate extreme humidity conditions grow on the grasslands here. Vegetation can be absent or be represented only by mosses and lichen at places. But there are also more biodiverse areas on the alvars and these are a good habitat for the protected orchids. Alvars that are not being grazed get overgrown and the species disappear. The alvars of the cape Sääretirp were restored during the project “Elu alvaritele” (Life to alvars).

In addition to the semi-natural communities, juniper forests and reeds are also characteristic to the island of Kassari. Both offer sites for nesting and refuge for birds. Many fish species spawn and feed in the reeds.

In conclusion, the vegetation in the protection area is very biodiverse due to the lime-rich soils and mild maritime climate. One of the most important value from the plants in the protection area is the population of the slender hare’s-ear (Bupleurum tenuissimum) that is the only population extant in Estonia. From the interesting species, also the low spikemoss (Selaginella selaginoides), dwarf mouse-ear (Cerastium pumilum) and small scabious (Scabiosa columbaria) that has become quite rare on the alvars grow here. Orchids can obviously be found on the semi-natural areas, for example the musk orchid (Herminium monorchis), flecked marsh orchid (Dactylorhiza cruenta), fly orchid (Ophrys insectifera), military orchid (Orchis militaris) and others.

Käina Bay
The area of Käina Bay is over 800 ha, comprising ⅕ of the protection area. There are about 15 small islands in Käina Bay dependent on the water level. The average depth of Käina Bay is only 0.5 metres. Thus, it is more a coastal lake than a bay. The mean salinity range is between 6–7%. 200 different bird species have been registered in Käina Bay and its surrounding areas. It is the most important nesting and migration site for water birds on the island of Hiiumaa. The protection area has been included among the bird areas of international importance. A large number of water and coastal birds stop in the area for resting and feeding purposes during spring and autumn. 1,000–5,000 birds stop in Käina Bay in the spring time, the amount may be more than four times higher in autumn.

Käina Bay is also the most important gathering place of the common crane (Grus grus) and greylag goose (Anser anser) on the island of Hiiumaa in autumn.

The most exciting nesters and peregrine birds are the white-tailed eagle (Haliaeetus albicilla), ruff (Philomachus pugnax), Southern dunlin (Calidris alpina schinzii), lesser white-fronted goose (Anser erythropus). You can hear the Eurasian bittern (Botaurus stellaris) here, but also meet the pied avocet (Recurvirostra avosetta), black-tailed godwit (Limosa limosa) and ruddy turnstone (Arenaria interpres)

The bays of Käina and Vaemla are important spawning sites for fish. 12 species of fish have been reported in the protection area. The main fish species are the Eurasian ruff, European perch and ide.

The medicinal mud that can be found in both Käina and Vaemla bays has accumulated during the last 2,000 years. The medicinal mud is being used for medicinal purposes as well as making cosmetic products.