The park takes next to all the catchment basin of the lake Vodlozero and river Ileksa the area of which amounts to 5,2 thousand of square km.
In the basin of the river Ileksa there are 407 reservoirs with the general size of 122 square km. All the lakes originate from the glacial period. Their kettles are not deep, saucer-formed, bottoms are flat and covered by thick silts.
Vodlozero Lake is the largest reservoir of the park with the size of 358 square km. The general length of the meandering shoreline makes up to 232 km, and including islands its 446 km. There are about 196 islands in the lake. The lake dates back to the glacier period and is noted for its shallowness, the maximal depth is 18 meters, and the average is 4 meters only.