Basically an extended channel of River Shuya and which is almost in an oval form, Lake Vagatozero covers an area of 24,5 sq. kms with the lake coast largely made up of morain and other products of erosion. Mostly, along the eastern coast sandy beaches are frequent along with agricultural lands often coming close to the shores. Five inflows pour into the lake are the biggest of these are River Shuya and River Sianga (Siapsia).
Lake Vagatozero is quite shallow reservoir with maximum depths of 8,5 m on the south-eastern parts of the lake. The ichtyofauna of Lake Vagatozero comprises of 18 species of fish including roach, pike and bream. Other species found within the lake are perch, white-fish, ide and salmon.. Dace, loach, chub, gustera, bullhead, sinets and ukleya, also dwell in the lake waters.