There are 2 natural reserves in the Park – Plokštinė (810 ha) and Rukundžiai (245 ha). Forestry, agriculture and any other economic activities as well as mushroom and berry picking and cognitive tourism are prohibited in these areas. It is allowed to visit them only on scientific research purposes having permit issued by the administration of the Žemaitija National Park.
The Plokštinė reserve is aimed to perserve standard complex of Plokštinė woods and marsh with ecosystems typical for this region, rare species of plants, mushrooms and animals, natural streams of Juodupis and Uošna and unique geomorphological structure of Plokščiai thermo-sinkhole.
Rukundžiai reservation preserves the unique natural complex of marshy woods of Aklaežeris and the stream of Pietvė.