Biological nitrogen fixation is a key process balancing the loss of combined nitrogen in the marine nitrogen cycle. Its relevance in upwelling systems is not fully resolved. This dataset contains rates of nitrogen fixation through the euphotic layer in two size fractions measured following Montoya et al (1996) technique. It also contains the stable isotopes of carbon in seston expressed in delta notation (δ13C, ‰, VPDB). We sampled in the region of the Guinea Dome and Equatorial Atlantic Ocean along 23°W during Meteor cruise M119 in September 2015. Water samples were collected by niskin bottles attached to a rosette equipped with CTD sensors. Incubations were done in on-deck incubators refrigerated by running surface water continuously and simulating the light intensity of each depth by neutral density filters or meshes.