The Waterbury Branch is served exclusively by shuttle trains running 6 to 7 times per day between Bridgeport and Waterbury, at one point in time the first train from Waterbury in the AM rush hour was extended to Stamford, but this has been discontinued at the time of writing during the COVID-19 pandemic. The COVID-19 pandemic also completely discontinued service on the branch (signal work was also being done on the line, including the installation of Passive Train Control) from April 6, 2020 until October 26, 2020, with shuttle buses replacing all train service.

Trains connect in Bridgeport with trains to New York (or New Haven) although the branch does not actually leave the main line until Devon junction, just after the New Haven main line crosses the Housatonic River, located between the Stratford and Milford Stations. Under the current timetable (as of Spring 2024) all weekday shuttle trains stop at Stratford and all weekend trains skipped Stratford. During construction a temporary Devon Transfer Station has been constructed (with no access to the outside world) for shuttle trains connecting with mainline electric trains.

The overall branch is rural and offers impressive views as trains run along the Naugatuck River (which combines with the Housatonic River at Derby) for much of it. The ride feels like it should be on a much longer Amtrak journey then a short Metro-North one. Every station on the line except Waterbury is unimproved, not accessible, and still has just low-level platforms.