Along its course it passes through Apple River Canyon State Park and the town of Hanover.

It flows into the Mississippi River about 7 mi (11 km) northwest of Savanna.

In Jo Daviess County, it collects two short tributaries known as the West Fork Apple River and South Fork Apple River.

Apple River was so named on account of the crabapple trees along its course.

[3] The river is part of the Driftless Area of Illinois, a region that was bypassed by the last ice age; "the glacial sweep which ironed out hills and filled valleys in other parts of the state left this area unscratched.