The source of the river is in swamps west of the settlement of Vaskelovo, and the Sestra flows in the general direction south, having its mouth in the town of Sestroretsk.
After the construction of a dam for the needs of the munitions factory in Sestroretsk, a part of the river was turned into a reservoir called Sestroretsky Razliv (Sestroretsk Overflow), 2 metres (7 ft) deep with an area of 10.6 square kilometres (4.1 sq mi).
The Sestroretsk Overflow is separated from the Gulf of Finland with a ridge of artificial sand dunes.
Excess water is dumped into the Gulf of Finland through a canal, which is 4.8 kilometres (3.0 mi) long.
It currently serves as a border between Vsevolozhsky (east, formerly Soviet Union) and Vyborgsky (west, formerly Finland) districts of Leningrad Oblast.