Motul de San José is located from the north shore of Lake Petén Itzá, in the centre of the department of El Petén. The nearest town is Flores, to the south, on the other side of the lake. The nearest villages are San José, away, and San Andrés, away, both are to the south of the site, on the northern shore of the lake. The archaeological site is connected to Nuevo San José, a northern expansion of San José, by a dirt road. It lies among land that has been cleared of forest within the last century and is now used to plant maize and graze cattle.