Its watershed covers 1,694 square miles (4,387 km2)[3] within a rural region of rolling hills and farmland southwest of Dubuque.

[4] The Maquoketa rises in southeastern Fayette County just southwest of Arlington in Fairfield Township, and approximately 10 miles (16 km) east of Oelwein.

It flows briefly northeastward, then generally southeastward through Clayton, Delaware, Jones and Jackson Counties, through Backbone State Park and the towns of Dundee, Manchester and Monticello.

It enters Pool 13[5] of the Mississippi from the southwest in eastern Jackson County a few miles upstream from Sabula approximately 30 mi (48 km) southeast of Dubuque.

[11] Along much of this stretch, the river flows through a canyon bounded by steep cliffs of Silurian dolomite.