The Baker River rises in the Cascade Range near Whatcom Peak, in the northern section of North Cascades National Park. 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. Many of these tributaries harbor tall, but never officially measured waterfalls. Most of the southern half of the river is impounded in artificial lakes, both part of the Baker River Hydroelectric Project. The first reservoir is -long Baker Lake, impounded by Upper Baker Dam. (The lake was formerly a natural lake, until its level was raised by the -high dam.) Lake Shannon, impounded by Lower Baker Dam, begins immediately below Baker Lake and stretches about downstream. Below Lower Baker Dam the Baker River flows unimpeded (except for a small weir at a fish passage station) for about a mile before emptying into the Skagit River.