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A new approach to automate the challenging task of defining the complexity level for conceptual modelling of micropollutant (MP) fate in sewer system is here presented. The approach combines GIS information and advanced statistical techniques (e.g., cluster analysis) and provides for a realistic description of in-sewer hydraulic residence time (HRT), which is fundamental for simulating MP removal processes occurring during in-sewer transport. The conceptual model was first tested in a full-scale catchment, where HRT distribution was determined based on spatial distribution of discharge sources and following calibration against high-frequency flow rate data. The model was then used to predict the dynamics of an ideal MP (biodegradation half-life = 2.5 h) at the outlet of the sewer system, revealing higher removal during in-sewer transport when considering an average HRT compared to a discrete HRT distribution. These results demonstrate that an intermediate complexity level, between highly detailed hydrodynamic models and simplified models, could be adopted for MP fate predictions while keeping computational demands reasonable. This latter aspect can be also of particular interest when an integrated modelling perspective (e.g., sewer and WWTP) is considered