 From its headwaters in the Coast Mountains , the Yukon River flows northwest , across the Yukon – Alaska border , until it intersects the Porcupine River at the settlement of Fort Yukon . At that point , the river turns west and southwest , flowing through the Yukon Flats , a low @-@ lying wetland area containing thousands of ponds , streams , and other small bodies of water . As the river flows southwest , it intersects the Tanana and Koyukuk rivers before looping south , then north into Norton Sound in the Bering Sea . 
