Microplastic (MP) pollution is an emerging issue in aquatic sciences. Rain and storm events are responsible for the mobilization and transport of a range of pollutants in aquatic systems, yet to date no study has examined how microplastic abundance changes in waterways during such events. The aim of this study was to determine how microplastic concentrations changed over the course of the storm event in an urban estuary. Sampling was conducted at high frequency before, during, and after a storm event that caused flooding in the Cooks River estuary, Australia. Microplastic abundance increased during two days of heavy rain from 400 particles m3 before storm event to up to 17,383 particles m3 after the event. Variation in microplastic abundance was positively related to five-day average antecedent rainfall. The results highlight the importance of rain and storm events as key moments of microplastic contamination in aquatic systems. The results have implications for considering the maximum number of microplastics that aquatic life may be exposed to and the importance of strategies to manage stormwater to minimize the input of microplastics to aquatic ecosystems.