It rises north ofLa Paz and flows northeast. TheMadre de Dios River is where its mouth is at. In the upper portion of its course, it flows through highland forest and rainforest, where the rapids ofCachuela Esperanza interrupt the upstream navigability of the river. The middle river runs through dense rainforest where it is joined by theMadidi River and theTuichi River which flow throughMadidi National Park. The Tuichi River joins the Beni River upstream from the townRurrenabaque. North of Rurrenabaque, the Beni River runs through theLlanos de Moxos also known as the Beni Savanna, which is named after the river. It empties into the larger Madre de Dios atRiberalta.
The Beni River has a number of minor tributaries, including intermittent streams such as the Emero River.[3][4]
In 1947, theCIA received unverified information that suggested there were settlements ofescaped Nazis along the Beni and its tributaries.[5]