The hyporheic zones (HZs) are key sites of the production of nitrous oxide (N2O), a potent ozone-depleting greenhouse gas. Denitrification is the primary process of N2O production in HZs, including four reduction steps (NO3−→NO2−→NO→N2O→N2). Electron competition occurs between the four reduction steps and can significantly impact the production of N2O. However, denitrification was typically considered as simplified two step reactions for investigating the release of N2O, neglecting the electron competition among the four-step reactions. Moreover, the N2O production/consumption patterns are regulated by both hydraulic and biogeochemical conditions in HZs. Dynamic microbial growth cannot only mediate the biogeochemical reactions, but also change hydraulic properties spatiotemporally by bioclogging. But microbial growth is rarely considered for investigating N2O dynamics of HZs. To assess these effects on hyporheic N2O dynamics and source-sink function, we establish a novel numerical model of N2O dynamics of HZs, coupling porous flow, reactive transport, electron competition, microbial growth and bioclogging. The results show that the weak electron competitiveness of N2O reductase results in a less allocation of electrons to the N2O reduction process, particularly in situations with limited carbon sources, thus increasing the release of N2O into the rives. Microbial growth significantly influences N2O release from HZs into rivers, increasing by more than two orders of magnitude on average compared to the model neglecting microbial dynamics. In contrast to the classical knowledges that HZs in coarse sediments tending to short residence time cannot act as sources of N2O, dynamic microbial growth obviously increases the potential for N2O release from HZs in coarse sediments to the rivers. The global Monte Carlo regional sensitivity analyses indicate that microbial biomass is the most critical factor determined the hyporheic source-sink function for N2O, followed by carbon oxidation rate and residence time. These are significantly different from previous knowledge that the residence time and oxygen/nitrogen uptake rate are the most sensitive parameters, which may lead to misunderstanding of the key controlling factors of N2O release from HZs. In addition, we propose a new Damköhler number (DaO2∗) of dissolved oxygen by multiplying the classical DaO2 with a dimensionless microbial modification factor for identifying N2O source-sink function of HZs, with DaO2∗ < 1 for N2O sink, while DaO2∗ > 1 for N2O source.