In its upper reaches, the river is known by several names: Río Quisil, Río Naranjo, Río Cocola, and Río Yula San Juan. It takes the name Río Ixcán in its middle and lower course.
The river flows northward, marking for several kilometers the natural border between the Guatemalan departments of Huehuetenango and El Quiché. Continuing north, it passes through areas inhabited by rural communities that use its waters for irrigation, fishing, and domestic purposes.
After a course estimated at about 200 kilometers, the Río Ixcán crosses the border into Mexico, in the state of Chiapas, at coordinates 16.074929°N, 91.107817°W. Here, it joins the Río Lacantún, a tributary of the larger Río Usumacinta system, which forms one of the most important river basins in the Mesoamerican region.
The Río Ixcán watershed covers an area of about 2,085 km² within Guatemalan territory. Its flow regime is typical of tropical rivers, with abundant discharge and pronounced floods during the rainy season, from May to October. Numerous mountain streams feed its upper course.
From an environmental perspective, the Río Ixcán flows through a region rich in tropical forests and biodiversity, part of the wider ecological area of the Selva Lacandona. Moreover, its confluence with the Lacantún lies close to sites of great historical and archaeological interest, including the remains of Sak-Bahlán, the ancient Maya stronghold.