The Amazon River is a major source of terrestrially-derived dissolved organic matter (DOM) to the Atlantic Ocean. Measurements of dissolved organic carbon (DOC) and its optical properties (absorbance and fluorescence) were made in the water within and adjacent to the Amazon River plume during two cruises conducted at periods of low (September–October/2011) and high (July/2012) river discharges. Four fluorescent components were resolved by excitation emission matrix fluoresces combined with parallel factor analysis (EEM-PARAFAC) as two terrestrial humic-like components, one marine humic-like component, and one autochthonous protein-like component. The distribution and dynamics of optically active fraction of DOM were largely controlled by physical mixing along the Amazon River-ocean continuum, with the exception of the protein-like component whose distribution was driven by factors other than dilution. Principal component analysis (PCA) enabled differentiation of water samples following gradient of terrestrial signatures and distinction of source materials associated with different fluorescent components. On board water incubation experiments with photochemical and microbial alterations revealed that photochemistry was primarily responsible for the removal of optically active fraction of DOM whereas the contribution of microbial transformation to this fraction was minor. Results from this work will provide a better understanding of DOM compositions and transformations in a globally significant river plume-ocean continuum. •Four fluorescent components are revealed in the Amazon River plume and ocean waters.•Physical mixing was the dominant driver for CDOM and humic-like fluorescent DOM.•Protein-like fluorescent component was controlled by factors other than dilution.•Photochemistry is more effective and efficient in degrading CDOM than microbes.