The island has 15–70 m high rocky cliffs, the lower relief down to the beach being dominated by conical mound-like stony structures.

The climate in the area is exceptionally severe, with prolonged, bitter winters, so that the waters of the Laptev Sea around Stolbovoy Island are covered by ice most of the year.

Tectonically deformed sedimentary rocks that accumulated during Late Jurassic to Early Cretaceous periods comprise Stolbovoy Island.

These rocks have been folded into a synclinal structure, thrust faulted, and intruded by small quartz diorite dikes.

All vegetation consists of dry to wet barren landscapes with scattered, herbs, lichens, mosses, and liverworts.