The most popular route into Guatemala by river is via the Río Usumacinta [1], which divides Mexico and Guatemala. Boats travel from the Mexican town of Frontera Corozal [2] to La Técnica and Bethel [3], in Guatemala’s northern Petén [4] department. This is the route of choice for travelers wanting to combine visits to the Mexican sites of Palenque [5] and Yaxchilán [6] with trips to the various Petén ruins.
Yaxchilán lies on the Mexican bank of the Usumacinta and is highly recommended. Buses from Palenque to the Mexican border are available via Transportes Montebello (and Autotransportes Rio Chancala. From La Técnica, buses leave for the Petén departmental capital of Flores at 4 a.m. and 11 a.m. ($4, five hours). Buses leave Bethel for Flores at 5 a.m., noon, 2 p.m., and 4 p.m., cost $4, and take four hours to make the trip. Package trips encompassing bus and boat transportation are available from various travel agencies in Palenque and Flores for travel in either direction for about $35.
It is also possible to travel from Benemérito, south of Frontera Corozal, up the Río La Pasión to Sayaxché, Guatemala, and via the Río San Pedro between La Palma and El Naranjo. These routes lack scheduled passenger service and are not recommended as they are increasingly being used as transshipment points by the growing drug and illegal immigrant trade between Petén and Mexico.
Links:
[1] http://www.moon.com/destinations/guatemala/peten/the-maya-biosphere-reserve/sierra-del-lacandon-national-park/rio-usumacinta
[2] http://www.moon.com/destinations/cancun-the-yucatan/the-state-chiapas/the-rio-usumacinta-valley/frontera-corozal
[3] http://www.moon.com/destinations/guatemala/peten/the-maya-biosphere-reserve/sierra-del-lacandon-national-park/bethel
[4] http://www.moon.com/destinations/guatemala/peten
[5] http://www.moon.com/destinations/brazil/minas-gerais/belo-horizonte/around-belo-horizonte/caverns/gruta-do-maquine
[6] http://www.moon.com/destinations/guatemala/peten/the-maya-biosphere-reserve/sierra-del-lacandon-national-park/yaxchilan