Conventional wastewater treatment plants are not designed to treat micropollutants; thus, for 20 years, several complementary treatment systems, such as surface flow wetlands have been used to address this issue. Previous studies demonstrate that higher residence time and low global velocities promote nutrient removal rates or micropollutant photodegradation. Nevertheless, these studies were restricted to the system limits (inlet/outlet). Therefore, detailed knowledge of water flow is crucial for identifying areas that promote degradation and optimise surface flow wetlands. The present study combines 3D water flow numerical modelling and liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS/MS). Using this numerical model, validated by tracer experimental data, several velocity areas were distinguished in the wetland. Four areas were selected to investigate the waterflow influence and led to the following results: on the one hand, the number and concentration of micropollutants are independent of the waterflow, which could be due to several assumptions, such as the chronic exposure associated with a low Reynolds number; on the other hand, the potential degradation products (metabolites) were also assessed in the sludge to investigate the micropollutant biodegradation processes occurring in the wetland; micropollutant metabolites or degradation products were detected in higher proportions (both number and concentration) in lower flow rate areas. The relation to higher levels of plant and microorganism metabolites suggests higher biological activity that promotes degradation.