With a watershed of approximately 270 square miles (700 km2) in a complex of deep valleys partially inside North Cascades National Park, it is the last major tributary of the Skagit before the larger river reaches its mouth on Skagit Bay.

The river flows through Concrete, Washington, near its mouth and has two hydroelectric dams owned by Puget Sound Energy.

It flows south, starting in the Baker River Valley north-east of Mount Shuksan.

The river flows generally southwest through a steep glacial valley, receiving several short glacial-fed tributaries from surrounding mountains.

[5] Since the 1990s, however, the population has recovered somewhat, in part due to improvements in the smolt trapping and transportation system.

Artificial enhancement began in 1896 when the State of Washington constructed a hatchery on Baker Lake.

[10] All returning sockeye are trapped below Lower Baker Dam and transported to the artificial spawning beaches.