There are 26 natural bigger and smaller lakes in the Park. The total area of them is 1484,2 ha. The largest lakes - the lake of Plateliai, Ilgis and Beržoras - occupy approximately 90 % of the total area. The conformation of the bottom of these lakes is very complex, there are islands in all of them (7 islands in the lake of Plateliai, 2 islands in the lake of Ilgis, 1 island in the lake of Beržoras). The most picturesque, cleanest and deepest lake in Žemaitija and the National park is the lake of Plateliai. Its area is 1205 ha, the average depth is 10,5 m, the deepest place is 47 m, the avarege level above the sea level is 146,5 m. The length of the coast is approximately 31 kilometers.
There are lots of small lakes in the territory of the Park, 22 of them are less than 5 ha; 10 are less than 1 ha.
The lakes of Burgis and Luoka have vegetations of Chara spp.. The lakes of Burgis, Burgalis and Skyplaičiai have lots of benthic vegetation of Chara spp. All the above mentioned lakes following the directive of vegetations of the EU may be attributed to the following type of vegetations - hard oligo-mesotrophic waters with benthic vegetation of Chara spp. The lakes of Vaivadė (Petreikis), Burgis, Endriuškaičiai, especially their turfy bays are full of Magnopotamion and Hydrocharition. There are lots of natural nourishment in these lakes They are attibuted to natural eutrophic lakes with Magnopotamion or Hydrocharition-type vegetation. There are small lakes surrounded by marsh in the Park, thery are attributed to natural dystrophic lakes. There is very little flora in them, the water is brown because of turf and humus accids. Such are small marshy lakes of Lestis, Piktežeris, Aklaežeris.
The biggest river of the National park the Babrungas takes its source from the lake of Plateliai; its length is 47,3 km, 10 km of it run through the territory of the Park. The longest river is the Uošna, its length is 16,6 km, 13,3 km of it run through the territory of the Park. Besides the mentioned rivers there are 32 rivulets in the Park, 17 of them of it run only in the territory of the Park. The total length of these rivultes is 103,5 km, approximately 30 rivulets take their source in the Park. Larger part of the rivers and rivulets of the National park (51%) have been reclaimed and straightened.
There are quite a few springs in the territory of the Park, some of them even have sacral meaning. Springs of Plokščiai (3,2 ha) and Pilelis (2,4 ha) are natural monuments. Visitors can easily reach the springs of St.John and Pilelis.