Lance Crawford made a pair of free throws to give Massachusetts-Lowell a 46-44 lead with 10:21 to play, and the River Hawks led the rest of the way. Banegas-Flores' trey stretched the lead to nine points, 63-51 with 1:57 left.
Christian Sengfelder's 3-pointer gave Fordham an early 13-4 lead. Massachusetts-Lowell answered with a 20-8 surge to take a 25-24 halftime lead.
Jahad Thomas scored 12 points, Chad Holley had 11 points and Kerry Weldon 10 for Massachusetts-Lowell (3-2), which has won three straight and will play its first home game Tuesday night against Mount Ida.