Maquoketa, IA. Online Offers. Maquoketa ( /ˌməkoʊkɨtə/) is a city in Clinton and Jackson counties in the U.S. state of Iowa. Located on the Maquoketa River, it is the county seat of Jackson County. U.S. Route 61 adjoins the city, which therefore benefits, or possibly hinders, from traffic between Dubuque and the Quad Cities. Iowa Highways 62 and 64 also pass through the city.