The Amazon river accounts annually for 20% of riverine discharge into the global ocean with strong seasonal variations. This lens of freshwater spreads at surface as a plume, and can reach as far as the Caribbean. During this journey, the changing physicochemical characteristics of the aging plume define contrasting plankton habitats. These habitats select for communities with varying degrees of complexity of the plankton food web. During RV METEOR cruise M174 (Voss, 2021) we studied the dominant trophic function at the base of the food web (autotrophs vs mixotrophs) using stable isotopes of nitrogen in specific amino acids as well as bulk isotopes of carbon and nitrogen. This dataset contains the nitrogen signatures of 12 amino acids in δ notation (δ15N, ‰ vs N2 in air), the mol% of 12 amino acids and the carbon (δ13C, ‰ vs VPDB) and nitrogen isotopes in bulk samples at surface as well as environmental data and phytoplankton community structure. Seston was separated into two size fractions, the picoseston comprised of particles below ca. 3µm (https://doi.pangaea.de/10.1594/PANGAEA.971293), and a mixture of nano- and microseston with particles above ca. 3µm (this dataset).