Rapid sand filters (RSF) are an established and widely applied technology for the removal of dissolved iron (Fe²⁺) and ammonium (NH₄⁺) among other contaminants in groundwater treatment. Most often, biological NH₄⁺oxidation is spatially delayed and starts only upon complete Fe²⁺ depletion. However, the mechanism(s) responsible for the inhibition of NH₄⁺oxidation by Fe²⁺ or its oxidation (by)products remains elusive, hindering further process control and optimization. We used batch assays, lab-scale columns, and full-scale filter characterizations to resolve the individual impact of the main Fe²⁺ oxidizing mechanisms and the resulting products on biological NH₄⁺ oxidation. modeling of the obtained datasets allowed to quantitatively assess the hydraulic implications of Fe²⁺ oxidation. Dissolved Fe²⁺ and the reactive oxygen species formed as byproducts during Fe²⁺ oxidation had no direct effect on ammonia oxidation. The Fe³⁺ oxides on the sand grain coating, commonly assumed to be the main cause for inhibited ammonia oxidation, seemed instead to enhance it. modeling allowed to exclude mass transfer limitations induced by accumulation of iron flocs and consequent filter clogging as the cause for delayed ammonia oxidation. We unequivocally identify the inhibition of NH₄⁺oxidizing organisms by the Fe³⁺ flocs generated during Fe²⁺ oxidation as the main cause for the commonly observed spatial delay in ammonia oxidation. The addition of Fe³⁺ flocs inhibited NH₄⁺oxidation both in batch and column tests, and the removal of Fe³⁺ flocs by backwashing completely re-established the NH₄⁺removal capacity, suggesting that the inhibition is reversible. In conclusion, our findings not only identify the iron form that causes the inhibition, albeit the biological mechanism remains to be identified, but also highlight the ecological importance of iron cycling in nitrifying environments.