Sinking diatom aggregates are important components of vertical elemental fluxes and represent ‘hotspots’ of microbial-driven remineralization in the water column. A combined analytical approach of microsensors and fluorometry was used to measure oxygen (O2) and ammonium (NH4+) concentrations in sinking diatom aggregates as a function of the ambient O2 concentrations. Diffusive fluxes of O2 and NH4+ within and around sinking aggregates were subsequently analyzed using a diffusion-reaction model. Diffusion limitation of O2 within the diatom aggregates occurred when ambient O2 concentrations decreased beneath 100 µM. At ambient O2 concentrations of 20 µM, the measured flux of O2 to aggregates was equivalent to 33% of fluxes when O2 concentrations were in equilibrium with the atmosphere and approximately 50% of the aggregate volume was anoxic. When the diatom aggregates were maintained under hypoxic conditions, NH4+ was produced in a ratio of -8.9 mole O2 consumed : 1 mole NH4+ produced which is within the expected range during ammonification. The average POC-specific respiration rate and the average PON-specific NH4+ production rate under hypoxic conditions were 0.065 d-1 and 0.052 d-1, respectively. Under anoxic conditions, the NH4+ release was 18% of that measured under hypoxic conditions. Our empirical and modeled data revealed diatom aggregates to be microenvironments of elevated NH4+ concentrations ranging from 1–8 µM and therefore to be potential sources of NH4+ in OMZs in the ocean.