[4] Chapin is in northwest Morgan County along U.S. Route 67, which crosses the north side of the village.

Illinois Route 104 runs concurrently with US 67 through Chapin, leading east to downtown Jacksonville and northwest 10 miles (16 km) to Meredosia.

Lick Branch rises within the village limits and flows northeast to Indian Creek, a northwest-flowing tributary of the Illinois River.

The northwest corner of the village is the source of one of the headwaters of Coon Run, which flows north then west to the Illinois River.

The southern half of the village is drained by south-flowing tributaries of Mauvaise Terre Creek, which flows west to the Illinois.