The airport covers 919 acres at an elevation of 1,749 feet. It has two runways: 12/30 is 6,898 by 100 feet concrete and 17/35 is 6,893 by 100 feet concrete. In 2013 the airport had 15,200 aircraft operations, an average 42 per day: 72% general aviation, 18% air carrier, and 10% air taxi. At that time 32 aircraft were based at this airport: 69% single-engine, 19% multi-engine, 6% jet, and 6% glider. From 2012 to 2018, runways 17/35 and 12/30 were overhauled using concrete, replacing worn out asphalt on both runways. The airport passenger terminal was renovated in 2009. The upgrades included an overhaul of the interior design and an expanded TSA inspection area. The airport has no jet bridge, as the turboprop planes that served the airport did not work with them. With the introduction of jet service to the airport in 2016 and the discussion of a possible new terminal building in coming years, the airport could acquire a jet bridge in the near future. Watertown is the only commercial airport in South Dakota without a jet bridge. The airport has free parking.
Airline flights at Watertown started about 1935, with a local company, Watertown Airways, operating scheduled service between Minneapolis–St. Paul International Airport and Watertown. This route continued through South Dakota with additional stops in Huron, Pierre, Phillip, Rapid City, and Spearfish. By 1938, Mid-Continent Airlines was operating a route from Minneapolis-St. Paul to Omaha, Nebraska, with Watertown as one of the intermediate stops. Upon the 1952 acquisition of Mid-Continent by Braniff International, Braniff took over the operation of this route until 1959. North Central arrived in 1957 and successor Republic left in 1985. The first jet flights were North Central DC-9s in 1968. Mesaba Airlines, operating as Northwest Airlink, and later, Delta Connection, served Watertown for years, with daily Saab 340s to Minneapolis/St. Paul. When Delta quit using the Saab 340 in December 2011, and announced the end of air service to Watertown, flights from Minneapolis temporarily used Delta's Canadair Regional Jet 200, until Great Lakes Airlines took over 4 months later. Great Lakes Airlines offered daily non-stop 19-seat Beechcraft 1900Ds to Minneapolis/St. Paul, until city officials voted to end the service, citing unreliability of the airline. Great Lakes ended service to the airport on September 30, 2015. On August 15, 2016, Aerodynamics, Inc. began flying to Watertown with daily service to Denver, via Pierre, using Embraer 145jet aircraft. However, the airline suspended all operations nationwide and ended flights to Pierre and Watertown on January 17, 2019. Air service to Watertown resumed on April 3, 2019 with SkyWest Airlines operating as United Express. Sun Country Airlines flew several seasonal charter Boeing 737-800s to Laughlin/Bullhead City International Airport in Arizona, known as "casino or gamblers' flights," in coordination with travel agencies in Watertown. These trips ended in 2015.
