Urban rainfall events can lead to the runoff of pollutants, including industrial, pesticide, and pharmaceutical chemicals. Transporting micropollutants (MPs) into water systems can harm both human health and aquatic species. Therefore, it is necessary to investigate the dynamics of MPs during rainfall events. However, few studies have examined MPs during rainfall events due to the high analytical expenses and extensive spatiotemporal variability. Few studies have investigated the occurrence patterns of MPs and factors that influence their transport, such as rainfall duration, antecedent dry periods, and variations in streamflow. Moreover, while there have been many analyses of nutrients, suspended solids, and heavy metals during the first flush effect (FFE), studies on the transport of MPs during FFE are insufficient. This study aimed to identify the dynamics of MPs and FFE in an urban catchment, using high-resolution monitoring and machine learning methods. Hierarchical clustering analysis and partial least squares regression (PLSR) were implemented to estimate the similarity between each MP and identify the factors influencing their transport during rainfall events. Eleven dominant MPs comprised 75% of the total MP concentration and had a 100% detection frequency. During rainfall events, pesticides and pharmaceutical MPs showed a higher FFE than industrial MPs. Moreover, the initial 30% of the runoff volume contained 78.0% of pesticide and 50.1% of pharmaceutical substances for events W1 (July 5 to July 6, 2021) and W6 (August 31 to September 1, 2021), respectively. The PLSR model suggested that stormflow (m3/s) and the duration of antecedent dry hours (h) significantly influenced MP dynamics, yielding the variable importance on projection scores greater than 1.0. Hence, our findings indicate that MPs in urban waters should be managed by considering FFE.