Žemaitija (Samogitia) National Park has been established to protect:

• The largest lakes and forest nature complex in the Žemaitija region, the scientifically important forested swamplands of Plokštinė and Rukundžiai, Plateliai Lake, the hydrographical complexes of Laumalenka and Šilinė, the impressive moraine (Miktyvai and Pučkoriai) and kame (Šarnelė, Jazdauskiškiai and Grigaičiai) landscapes typical of this region, Gardai esker, Medsėdžiai and Liepija glaciolacustrine kames, the Babrungas and Mergupys valleys, the Paburgė, Siberija, Pakastuva, Užpelkiai, Ertenys and Paparčiai wetlands, the unique Paplatelė, Šeirė and Pailgys forests, the biotic communities of the Juodupys wet grasslands, rare and disappearing species of flora and fauna, as well as other natural complexes and objects.
• The particularly valuable and elaborate archeological complex of the north Žemaitija region featuring the Mikytai, Šarnelė, Pučkoriai, Gegrėnai, Pagardenys and other castle mounds and ancient ritual hills, the ancient Šventorkalnis settlement and castle site, the Žemaičių Kalvarija (Gardai) urban complex and religious architecture ensemble, the Plateliai manor and park complex, the villages of Beržoras, Stribaičiai and Visvainiai that have retained elements of great ethnocultural value, as well as other cultural heritage objects;
• The stability of the north western Žemaitija region‘s watershed ecosystem, its biotic components and their diversity.  

Almost the entire life in the Žemaitija (Samogitia) National Park is centered around the Plateliai Lake. It is the deepest, largest and probably the most beautiful lake in Samogitia with islands, peninsulas, bays, surrounded by hillsides and forests. It is home to the relict fish Coregonus lavaretus holsatus. The national park is rich with dense, shady spruce forests, natural old conifer and mixed tree forest. The abundance of castle mounds, sacred hills and sacred places are the reminders of the old culture. The small chapels and road shrines scattered by the roads and in the fields reflect the lifestyle and traditions of the local people. The old customs are especially emphasized during the traditional Shrovetide festival.

The park is dominated by hill, ridge- rich relief, deep lake waterholes, including the deepest in Žemaitija Plateliai Lake with the cobweb of shoals, islands, and peninsulas. The Plateliai Lake as well as other lakes and rivers are surrounded by forests and wetlands.

The National Park is distinguished by its legendary natural heritage objects: seven islands of Plateliai Lake, Kreiviškės and Auksala peninsulas, and the mysterious islands of Beržoras and Ilgis Lakes. The national park is rich with dense, shady spruce forests, natural old conifer and mixed tree forests also called the Western Taiga. The latter are protected in the entire Europe. Wetlands are rich with various species of organisms. Raganos Ash Tree is the thickest ash tree in Lithuania. In the national park, there are nesting places of the protected in Europe rare bird species (Bonasa bonasia, Crex crex, and Cygnus cygnus), and also relict plant species from the glacial period. Plateliai Lake is home to the relict fish Coregonus lavaretus holsatus. The cultural heritage of the National Park consists of castle mounds, ancient shrines (sacred hills), burial sites, and sites of ancient settlements. Among the most interesting are the Užpelkiai, Gegrėnai, Pūčkoriai, Jazdauskiškiai, Grigaičiai, St. John’s (Žemaičių Kalvarija), Šarnelė, Mikytai castle mounds; the Visvainiai, Mikytai, Vilkai, Gilaičiai, Paparčiai sacred hills, sites of ancient settlement in Gegrėnai and Šarnelė. Standing out with architectural uniqueness are the Žemaičių Kalvarija Church, and Babrungėnai Mill. 

This is a national park of a complex landscape structure characterised by exclusive uniqueness and abundance of the natural and cultural heritage objects as well as large recreational and educational tourist potential. It represents the landscape of Samogitia upland hill massifs, wetland massifs, the most distinctive in Samogitia the Plateliai (Virkšta) lake, and the settlements of Plateliai, Beržoras and Gardai (Žemaičių Kalvarija) which have retained their historical-urban value. The Samogitia National Park is classified under the top category from the perspective of exceptional value of the landscape. The landscape diversity of the Samogitia National Park has been created by the following major landscape types: large terraced forested and little cultivated lake waterhole, forested and little cultivated lakes, forested kame hill fields, forested kame terraces, forested and cultivated hill massifs and ridges, forested drumlinized morainic hill massifs, forested morainic small hill strip; transition, mixed and raised bog complexes, forested erosional valleys and slopes, wetland laky waterholes, natural and channeled streams, ethno-cultural settlements, standard settlements and former military complexes.

Territories of the European Community importance found in the Žemaitija National Park: 3140 Hard oligo-mesotrophic waters with benthic vegetation; 3150 Natural eutrophic lakes with Magnopotamion or Hydrocharition – type vegetation; 3160 Natural dystrophic lakes and ponds; 6230 Species-rich Nardus grasslands, on silicious substrates in mountain areas (and submountain areas in Continental Europe); 6410 Molinia meadows on calcareous, peaty or clayey-silt-laden soils (Molinion caeruleae); 6450 Northern boreal alluvial meadows; 7110 Active raised bogs; 7140 Transition mires and quaking bogs; 7210 Calcareous fens with Cladium mariscus and species of the Caricion davallianae; 7230 Alkaline fens; 9010 Western Taiga; 9020 Fennoscandian hemiboreal natural old broad-leaved deciduous forests (Quercus,Tilia, Acer, Fraxinus or Ulmus) rich in epiphytes; 9050 Fennoscandian herb-rich forests with Picea abies; 9080 Fennoscandian deciduous swamp woods; 91D0 Bog woodland; 91E0 Alluvial forests with Alnus glutinosa and Fraxinus excelsior.

The total number of plant species is 1031 of which 4 are protected by the European Community, and 51 are included in Lithuania’s Red Data Book. The total number of animal species is approximately 2500. Mammals – 50, of these 2 are protected by the European Community, and 5 are included into the Lithuania’s Red Data Book. Birds – 209, of these 52 are protected by the European Community,

and 56 are included into the Lithuania’s Red Data Book. Fishes – 34, of these 5 are protected by the European Community, and 2 are included into the Lithuania’s Red Data Book. Amphibians and reptiles – 15, of these 7 are protected by the European Community, and 3 are included into the Lithuania’s Red Data Book. Invertebrates – 2,130, of these 7 are protected by the European Community, and 24 are included into the Lithuania’s Red Data Book. 

The following reserves have been established in the Žemaitija National Park to protect its natural and cultural values: 2 strict nature reserves and 27 reserves (12 landscape, 3 geomorphological, 1 hydrographical, 1 botanical, 1 botanical-zoological, 3 telmological, 1 archaeological, 1 ethno-cultural, and 2 urban reserve(s)).

The strict nature reserves in the national park have been established to protect the following: Plokštinė – the Plokštinė forest and wetland complex formed in the Plokščiai thermokarst waterhole of a unique geomorphological structure with the natural Juodupis and Uošna streams, the water, grassland, wetland, and forest habitats of the European Community importance with the habitats of the typical plant, fungi, and animal species; Rukundžiai – the natural Rukundžiai complex of swampy and forested sinks of natural hydrogprahic structure; the wetland and forest habitats of the European Community importance with the typical flora and fauna; and habitats suitable for Leucorrhinia pectoralis, Lycaena dispar, Bonasa bonasia, and Lynx lynx. The landscape reserves have been established to protect: Beržoras – the especially distinctive landscape of the Beržoras village having retained the traditional features, Beržolas Lake and the surrounding area with the Beržoras village urban structure and architectural values, Beržoras Lake islands and open lakeshores; the forest and wetland habitats of the European Community importance; habitats suitable for Liparis loeselii, Crex crex, and other protected species; Grigaičiai – the distinctive Grigaičiai forested agrarian landscape typical of Samogitia with the Surbliai grave field, and habitats suitable for Crex crex, Cygnus cygnus, and other protected species; Jazdauskiškiai – the hilly agrarian forested landscape typical of Samogitia with the traditional system of land use and development, Žerniai and Jazdauskiškiai castle mounds, Jazdauskiškiai cemetery and grave field; water habitats of the European Community importance and the communities of typical plant and animal species; Laumalenkos – the unique natural Laumalenkos complex of peninsulas, islands, bays, junctions, lakes, forests and wetlands with the water, wetland, and forest habitats of the European Community importance with the communities of typical plant and animal species, nesting places of the protected birds; Mikytai – the distinctive hilly mosaic landscape typical of Samogitia with forests, fields, grassland, small interhill swamps and individual homesteads, the Mikytai castle mound, the Mikytai and Gudaliai sacred hills, Mačiūkiai grave field and mythological Laumė stone; wetland habitats of the European Community importance with the typical fauna and flora, and the communities of protected species; Paburgė – the typical landscape of forested and laky swampy waterholes with the water, grassland, wetland, and forest habitats of the European Community importance, and the protected animal and plant species; Plateliai – the landscape of the largest and deepest in Samogitia Plateliai Lake and the surrounds with the valuable coastline, islands, Kumelkaktė peninsula, Šventorkalnis archaeological complex, ancient settlements of the Ąžuolų island, and objects of underwater heritage; wetland, grassland, and forest habitats of the European Community importance, and habitats suitable for Hamatocaulis vernicosus, Liparis loeselii, Bonasa bonasia, and Lutra lutra, and other protected species; Pučkoriai – the landscape of the Pučkoriai morainic landform section with the especially distinctive mosaic of hills, groves, areas between hills and swamps, Pučkoriai II and Pučkoriai III mounds, old cemetery, Visvainiai sacred hill; wetland habitats of the European Community and the communities of the protected birds and insects; Babrungas – the landscape of the Babrungas and Uošna River valleys with the natural river and stream sections, the typical Babrungėnai village lakeside homesteads, Grigaičiai castle mound, Babrungėnai water mill and old cemetery; habitats suitable for the species of the European Community importance – Lycaena dispar, Unio crassus, Crex crex, Lutra lutra, and other protected species; Liepijos – the exemplary plateau-like hill landscape characteristic of the Mid-Samogitian upland with large Liepijos glaciolacustrine plateau-like hill and mixed Liepijos forest biocenoses; grassland, forest, and wetland habitats of the European Community importance as well as communities of the protected animal species; Stirbaičiai – the landscape of the Stirbaičiai village having retained the traditional features and traditional structure of land use and development, and elements of ethno-architecture; grassland, forest, and wetland habitats of the European Community importance, and communities of the protected plant and animal species; Šarnelė – the distinctive landscape of the Šarnelė kame landforms with the Šarnelė castle mound, ancient settlements, the site of the poet Vytautas Mačernis house and grave; grassland habitats of the European Community importance, and protected insect and bird species. The geomorphological reserves have been established to protect: Gardai – the remaining part of the Gardai esker with the protected species and habitats; Margupis – the particularly distinctive system of the Margupis Stream and its tributary valleys with the characteristic slope biocenoses, and the protected species and habitats; Medsėdžiai – the exemplary plateau-like hill landscape characteristic to the Plateliai pool – Medsėdžiai glaciolacutrine kame – with the habitats of the protected insect species. The Šilinė Hydrographical Reserve has been established to protect the exemplary landscape of the natural forest stream – the Šilinė Stream with its hydrographical structure and hydrological regimen, forested valley and sub-valley with natural grassland, springs, protected species and the water and forest habitats of the European Community importance.