Although the river's natural course runs northwest to its mouth at the Caribbean Sea, its waters also flow, via the canal's locks, into the Gulf of Panama to the south.

The terrain of the upper Chagres drainage basin is rugged, with its mountain slopes exceeding 45 degrees in 90 percent of its territory.

Gatun Lake encompasses approximately 470 square kilometres (180 sq mi), a vast tropical ecological zone part of the Atlantic Forest Corridor.

It is believed that the Cichla pleiozona species of peacock bass was introduced by accident to Gatun Lake by a Panamanian aquarist and doctor in 1958.

Locally called Sargento, these bass are not a native game fish of Panama but originate from the Amazon, Rio Negro, and Orinoco River basins of South America, where they are called Tucanare or Pavon and are considered a premier game fish.

Goods were transported on foot from Panama City to the town of Cruces on the rio Chagres, and from there by sailboats on the river all the way to its mouth.

Not much attention was focused on the river until the late 19th century, this time as part of the planning for construction of the Panama Canal.