The Amazon River is known as a region of intense biochemical reactivity. As a result of increased anthropogenic impacts in its catchment (e.g. population growth, agriculture, and deforestation), The Amazon River is undergoing fundamental changes. The RV METEOR cruise M174 (doi:10.1594/PANGAEA.935041) aimed to provide an integrated overview of nitrogen cycling processes in areas influenced by the Amazon River, which is crucial to estimate the ecosystem's health and productivity. During this cruise, six stations were visited to explore the significance of denitrification as a dominant pathway in the watercolumn of the Amazon and Pará estuaries. This dataset presents the stable isotopic composition of nitrate (d15N- d18O-NO3), as well as d2H and d18O of ambient water.