Riverine dissolved organic carbon (DOC) contains charcoal byproducts, termed black carbon (BC). To determine the significance of BC as a sink of atmospheric CO2 and reconcile budgets, the sources and fate of this large, slow-cycling and elusive carbon pool must be constrained. The Amazon River is a significant part of global BC cycling because it exports an order of magnitude more DOC, and thus dissolved BC (DBC), than any other river. We report spatially resolved DBC quantity and radiocarbon (Δ14C) measurements, paired with molecular-level characterization of dissolved organic matter from the Amazon River and tributaries during low discharge. The proportion of BC-like polycyclic aromatic structures decreases downstream, but marked spatial variability in abundance and Δ14C values of DBC molecular markers imply dynamic sources and cycling in a manner that is incongruent with bulk DOC. We estimate a flux from the Amazon River of 1.9–2.7 Tg DBC yr−1 that is composed of predominately young DBC, suggesting that loss processes of modern DBC are important.