Nitrate and ammonium are common inorganic contaminants of anthropogenic origin in many shallow aquifers around the world, while nitrite is less common, but it is most harmful than nitrate and ammonium due to its high reactivity. This paper presents evidence of nitrite accumulation after intense rainfalls in soil samples collected in an agricultural field characterized by organic matter chronic depletion. Moreover, an intact core from the same site was also collected to perform an unsaturated column experiment (60 cm long and 20 cm outer diameter) mimicking heavy rainfalls (230 mm in 2 days). Results from the field site showed nitrite accumulation (up to 0.45 mmol/kg) at 50–70 cm depth, just below the plough layer. The column experiment showed very high initial concentrations of nitrate and nitrite in the leachate and a progressive decrease of nitrate due to denitrification. The numerical flow model was calibrated versus the observed volumetric water contents and leachate flow rates. The numerical reactive transport model was calibrated versus the leachate concentrations of six dissolved species (ammonium, nitrate, nitrite, dissolved organic carbon, chloride and bromide). The optimized model resulted to be robustly calibrated providing insights on the kinetic rates driving the production, accumulation and leakage of nitrite, showing that incomplete denitrification is the source of nitrite. As far as the authors are aware, this is the first study reporting a clear link between high nitrite leaching rates and extreme rainfall events in lowland agricultural soils depleted in organic matter. The proposed methodology could be applied to quantify nitrite cycling processes in many other agricultural areas of the world affected by extreme rainfall events. Display omitted •Field monitoring was unable to give insights on NO2− accumulation.•Column experiments were unavoidable to truthfully describe NO2− fate.•Soluble salts were dissolved and leached by intense rainfalls.•Partial nitrification and denitrification produced a transient NO2− accumulation.•Droughts followed by extreme rainfalls will trigger NO2− leaching to groundwater.