Quantifying the different sources of nitrogen (N) within the N cycle is crucial to gain insights in oceanic phytoplankton production. To understand the controls of primary productivity and the associated capture of CO2 through photosynthesis in the southeastern Indian Ocean, we compiled the physical and biogeochemical data from four voyages conducted in 2010, 2011, 2012, and 2013. Overall, higher NH4 assimilation rates (~530 μmolm-2 h-1) relative to NO3 assimilation rates (~375 μmolm!2 h!1) suggest that the assimilation dynamics of C are primarily regulated by microbial regeneration in our region. N2 fixation rates did not decline when other source of dissolved inorganic nitrogen were available, although the assimilation of N2 is a highly energetic process. Our data showed that the diazotrophic community assimilated ~2 nmol N L!1 h!1 at relative elevated NH4 assimilation rates ~12 nmol L-1 h-1 and NO3 assimilation rates ~6 nmol L!1 h!1. The small diffusive deep water NO3 fluxes could not support the measured NO3 assimilation rates and consequently point toward another source of dissolved inorganic NO3. Highest NO2! values coincided consistently with shallow lower dissolved O2 layers (100–200 m; 100–180 μmol L-1). These results suggest that nitrification above the pycnocline could be a significant component of the N cycle in the eastern Indian Ocean. In our analysis we provide a conceptual understanding of how NO3 in the photic zone could be derived from new N through N2 fixation. We conclude with the hypothesis that N injected through N2 fixation can be recycled within the photic zone as NH4 and sequentially oxidized to NO2 and NO3 in shallow lower dissolved oxygen layers.