B. amazonicus is a benthopelagic (ecological region at the lowest level of water body) species that inhabits streams and lakes. The larvae of B. amazonicus are found in the main stem of the Amazon River, and possibly in other high-nutrient tributaries. Juveniles live in the adjacent floodplain, mostly under the floating macrophytes (floating or submerged aquatic plants)). Adults are distributed throughout the floodplains, including the flooded forests of white and black water rivers.

The migration of this species is complex. Near Manaus, B. amazonicus joins multi-species schools and migrates downriver from the Negro River to spawn in the Amazon River in December and January, as water levels there begin to rise. A similar pattern was also observed for Brycon sp. in the Madeira River. The embryos and larvae develop while drifting in the Amazon River, and probably get washed into the white water floodplains. After spawning (February to March) the adult fish return to the black-water tributaries. Later in the year (May to August) these fish move downstream again from the Negro River or other nutrient-poor tributaries into the Amazon or Madeira rivers, where they remain until the end of the wet season in September. At this time, they move upstream again to the next nutrient-poor tributary and into forest streams, where they spend the dry season before the next spawning migration (Araujo-Lima and Ruffino 2004).

Plant material is an important part of the diet of adult Brycon species; and thus these fish play a role in the dispersal of plants whose fruits they eat (Berra 2001).