Gananoque lies directly on three of Canada's busiest transportation routes: the four-lane Highway 401, the double-track Canadian National Railway main line, and the St. Lawrence Seaway. It is also home to a rich provincial highway heritage, being home to the remaining stretch of Highway 2. It is also the western terminus of the Thousand Islands Parkway, and a short drive from the Thousand Islands Bridge, which crosses into the United States as Interstate 81. Gananoque is served by the Gananoque Airport for general aviation.
Historically, the Gananoque River's watershed had been an important water transportation corridor, extending north to the Rideau River watershed and playing a key role in the town's early history and economic importance. In 1830, water was diverted near Newboro to the Cataraqui River as part of the Rideau Canal, sending this traffic instead to Kingston.
A four-mile short line railroad once linked the main CN Rail tracks to the heart of the village; the Thousand Islands Railroad terminated near the town hall
