Many Maya sites were built far away from rivers, but some others were built right on the river basins, mostly to control trade routes. The most important navigable rivers in the Maya World are the Usumacinta River (with sites such as Piedras Negras and Yaxchilan), the Pasion River (with sites such as Ceibal and Altar de Sacrificios) and the Motagua river (Quirigua was right on its course). There is no conclusive evidence that the Copan River was ever navigable, no dock was found by the early explorers, and no traces of any long distance trading canoes produced in the course of studies at the site. However, it is possible that it was indeed navigable.

One thing is clear, though. The inhabitants of Copan had abundant access to water resources and were knowledgeable in irrigation techniques used extensively on their agricultural fields, as finds in the Copan Forest (El Bosque) close to Las Sepulturas complex seem to indicate. The impact of the Copan River's movements is interesting to note, as will be discussed in the next paragraph, but without any shadow of doubt the river played an important part in the peopling of the Copan Valley, their agriculture, and as a resource for the Copan engineers and architects in planning their city and their constructions. Surely, considerations as to the proper management of this precious resource were made.

The Copan River's flow was diverted in the 1930's due to its proximity to Copan's Structure 21, with the passage of time the river had eaten away part of this structure destroying it at an alarming rate. Early explorers noted this phenomenon but were unable to intervene until the technology was available to challenge Mother Nature by altering the course of one of her rivers. Even though the destruction caused by the river is truly a tragedy it did come with a silver lining, as in eating away at the Structure 21's side the river managed to reveal important information about the construction phases at Copan. The various layers of stone upon stone that make up the bulk of this great structure can be clearly seen: it is called the Archaeological Cut and it revealed substantial information which shed a new light on the approach to the study of Copan's architecture.