AbstractMajor storms, which are increasing in frequency due to climate change, flush pollutant nutrients, including phosphorus (P), from river catchments through estuaries to the coast. Changes in P speciation alter the potential for P removal in sediments. We measured suspended particle matter (SPM), dissolved and particulate phosphorus and other physicochemical parameters at two river outlets of the Jiulong River (SE China) and a fixed station in the estuary during an entire storm (June 2019). During the storm, riverine total particulate phosphorus (TPP) more than doubled to approximately 100 μg P L−1 mainly from pollutant sources, while increased soil erosion reduced the TPP:SPM ratio by 1/3. The riverine DIP increase during the storm was only moderate (approximately 25%). As the storm intensified, the fresh‐brackish water interface moved downstream. There was increased SPM and TPP flux (up to approximately 25,000 kg P d−1) from resuspended surficial sediment that had been deposited during normal flow in the adjacent tidal flats and mangrove areas. These sediments had acted as microbial incubators. Reduced Fe in the resuspended sediment was converted to labile Fe oxyhydroxides in the oxic water column, which adsorbed DIP (and probably also DOP) and increased labile TPP exported downstream. During the storm, the total flux of riverine dissolved nutrients increased while the TDN:TDP ratio decreased from 43:1 to 32:1. Our study showed that estuaries are locations for temporary deposition of labile TPP during normal flow, which are flushed out during major storms, likely resulting in increased eutrophication, including encouraging harmful algal blooms in coastal zones.