Motul de San José lies on a limestone plateau at the northern edge of the fault depression that underlies the central lakes of the Petén Basin. The local topography consists of ridges, generally running east–west or northeast–southwest alternating with lower-lying areas with clay soils. These low-lying areas tend to feed into drainage systems flowing into either Lake Petén Itzá itself or into the Akte River. The Kantetul River is a seasonal watercourse with its origin to the northeast of the site and flowing westwards into the Akte River, passing from the site core. The Akte River in turn flows west into the San Pedro River, which flows northwest into Mexico where it joins the Usumacinta River and ultimately empties into the Gulf of Mexico. A mixture of ancient and modern agricultural terraces line the riverbank, north of the site core. Access to water was crucial for Maya cities, since much of the Maya lowlands have been described as a seasonal desert due to the combination of a prolonged dry season lasting between four and six months together with the limestone geography that makes surface water scarce. In addition the Maya greatly preferred water to land transport and used canoes to trade extensively by river and sea, and access to river routes connected cities to extensive trade routes.