The western branch of the river flows southeasterly in a wide "S" pattern from near the Monroe border with Newtown, Connecticut.

Less than a mile south of that point in Trumbull, a tributary called North Farrars Brook joins the Pequonnock.

Hedgehog Creek and Belden Brook in Trumbull flow into the river southwest of the intersection of Route 25 and Daniels Farm Road.

[10] Bridgeport Trumbull Prior to the arrival of Europeans, the Pequonnock Indians of the Paugussett nation lived on the banks of the river.

[23][24] The railroad was ripped up and replaced with Connecticut Route 25 up to Trumbull, north of which became Pequonnock River Valley State Park.

Results concluded that the river is to be considered class B (on the Connecticut Department of Environmental Protection rating system[36]) from the watershed through Trumbull and to the entry of Bunnell Pond in Bridgeport.

Areas further south on the river such as the Washington Street Bridge and into Bridgeport Harbor have considerably higher levels of e.coli and are correspondingly more polluted.