<p>Nitrite is a key intermediate in both aerobic and anaerobic nitrogen-cycling pathways. Although it rarely accumulates in the ocean, nitrite reaches micromolar concentrations in anoxic zones for reasons that remain unclear. Microorganisms are responsible for the production and consumption of nitrite, and their interactions are fuelled by the dynamic supply of organic substrates to anoxic waters. Here we use a mechanistic ecosystem model to study the microbial community response to such variations in the supply of organic matter over time. Our results demonstrate that nitrite-oxidizing bacteria, despite consuming nitrite, contribute to this accumulation through interactions with other microorganisms, mainly denitrifiers. Aerobic nitrite-oxidizing bacteria capitalize on the nitrite produced by nitrate-reducing denitrifiers, outcompeting and suppressing nitrite-reducing denitrifiers. Oxygen limits nitrite-oxidizing bacteria before all the nitrite is consumed, leading to nitrite accumulation. In an eddy-resolving, three-dimensional model, this shift in microbial activity in time manifests as shifts in both time and space, closely matching observed depth profiles of nitrite, its fluxes and the abundance of nitrite-oxidizing bacteria. These results reveal a mechanism driving nitrite accumulation, which maintains the standing stock of bioavailable nitrogen in anoxic zones, demonstrating that microbial interactions within fine-scale ocean currents dictate the fate of nitrogen.</p>