It originates in the muskeg of north western Alberta, flows west to British Columbia, then curves northward and returns to Alberta, where it follows a north-northeast course towards the Northwest Territories.

After passing over two main waterfalls, the Alexandra Falls and Louise Falls, it flows through the town of Hay River and discharges into the Great Slave Lake.

From there, its waters are carried to the Arctic Ocean by the Mackenzie River.

The Hay River effectively flows through the Hay-Zama Lakes.

At the Alberta – Northwest Territories border, the annual discharge is 3,630,000 cubic decametres (2,940,000 acre⋅ft).