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 (https://doi.org/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, a MUC was deployed at eight stations to collect short sediment cores, in order to explore the influence of the river on sediments. This dataset presents the results of nutrient fluxes at the sediment-water interface measured via incubation experiments.