Combined sewer overflows (CSOs) are an important pathway of organic micropollutants from urban areas to open water bodies. Understanding the temporal dynamics of these micropollutants during overflow events is crucial for applying appropriate sampling methods and implementing effective management strategies. Yet, little is known about the dynamics of micropollutants in CSOs, because most studies report concentrations from single grab samples or event mean concentrations (EMCs). With unique high temporal resolution measurements (3 minutes), we show the real dynamics of polar organic micropollutants in CSOs of one small (2,700 people: P) and one large (159,000 P) urban catchment, for two micropollutant categories: (i) 33 micropollutants in municipal wastewater and (ii) 13 micropollutants from urban surface runoff. The concentration dynamics depend on the substance source and the catchment size. Indoor substances such as pharmaceuticals show high temporal dynamics with changes of 1–2 orders of magnitude within 9 minutes in the CSO of the small catchment. In contrast, outdoor substances at the small catchment and all substances at the large catchment display considerably lower variation. We tested various time-proportional sampling strategies to assess the range of error when estimating EMCs. We recommend an interval of 3 minutes to capture the dynamics of indoor substances in CSOs from small catchments. The results highlight that both future monitoring campaigns and the planning and management of urban wet-weather treatment systems will benefit from high temporal sampling resolutions, not only to understand dynamics but also to minimize errors of estimated EMCs.