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.