The Magalloway River rises near the extreme northwestern corner of Maine, at the juncture of the West Branch and the Second East Branch of the Magalloway. The river flows south through logging country to 2.5-mile-long Parmachenee Lake, then descends for another 2.6 miles to the 15-mile-long Aziscohos Lake. Below the lake dam, the Magalloway turns west and descends 250 feet in two miles to the village of Wilsons Mills, Maine, before once again turning south, now along the New Hampshire-Maine border. The river ends where it joins the outlet of Umbagog Lake, forming the Androscoggin River.
Tributaries of the Magalloway include the West Branch, the Second East Branch, the First East Branch, the Little Magalloway River, and the Dead Diamond River. The Magalloway passes through the townships of Parmachenee, Lynchtown, Parkertown, Lincoln, and Magalloway Plantation in Maine, and the townships of Second College Grant and Wentworth's Location in New Hampshire.