Pierre and Watertown-area travelers have been experiencing scheduling difficulties after Great Lakes Aviation suspended flying operations.

The airline’s partner Aerodynamics Inc., or ADI, will continue operating the Great Lakes Jet Express flights between Denver, Colorado, and Pierre and Watertown, but the booking has become more complicated.

United, Delta and American airlines at the Denver airport told passengers this week that they can’t honor tickets from Pierre made through Great Lakes Aviation’s booking system. Pierre passengers flying to a connecting flight in Denver will instead need to cancel that leg, get a refund and re-book the leg through ADI as a separate flight.

Great Lakes had been decreasing the number of cities it serves, but the company announced Monday it’s immediately discontinuing air routes.