Hydroxylamine (NH2OH) is an important intermediate of nitrification and can contribute to nitrous oxide (N2O) production through abiotic and biotic pathways. NH2OH concentrations and associated biogeochemical controls in estuarine water and sediments remain poorly understood. Here, we investigated spatial and seasonal variability of NH2OH concentrations in water and sediments and determined the correlation between NH2OH and N2O in the Min River Estuary off southeast China. NH2OH concentrations in water and sediments ranged from 0.22 to 140 nmol N L−1 and from 0.17 to 9.22 μmol N kg−1, respectively. High differences in NH2OH concentrations between sediments and water could drive diffusion of NH2OH from sediments to water. NH2OH concentrations were significantly higher in warm than in cold seasons, suggesting that NH2OH production is highly dependent on temperature. Upper estuary (urban section) showed higher NH2OH concentrations in water and sediments, followed by lower and middle estuary. Temperature, dissolved oxygen, and pH were the major factors driving spatial and seasonal variability in NH2OH concentrations. Water dissolved N2O concentrations and air‐water N2O fluxes varied between 1.52 and 55.9 nmol N L−1 and between −57.7 and 78.7 nmol N m−2 h−1, respectively, with switches from net sinks in spring to net sources of N2O emissions in other seasons. Although N2O concentrations and fluxes were linearly correlated with water NH2OH concentrations, the contribution of NH2OH to N2O production could not be addressed. Therefore, the dynamics of NH2OH concentrations are a useful tool to assess potential production and consumption pathways of N2O in estuarine and coastal ecosystems.