Land-based micropollutants are the largest pollution source of the marine environment acting as the major large-scale chemical sink. Despite this, there are few comprehensive datasets for estimating micropollutant fluxes released to the sea from river mouths. Hence, their dynamics and drivers remain poorly understood. Here, we address this issue by continuous measurements throughout the Rhône River basin (∼100,000 km2) of 1) particulate micropollutant concentrations (persistant organic micropollutants: polychlorobiphenyls [PCBi] and polycyclic aromatic hydrocarbons [PAHs]; emerging compounds: glyphosate and aminomethylphosphonic acid [AMPA]; and trace metal elements [TME]), 2) suspended particulate matter [SPM], and 3) water discharge. From these data, we computed daily fluxes for a wide range of micropollutants (n = 29) over a long-term period (2008-2018). We argue that almost two-thirds of annual micropollutant fluxes are released to the Mediterranean Sea during three short-term periods over the year. The watershed hydro-climatic heterogeneity determines this dynamic by triggering seasonal floods. Unexpectedly, the large deficit of the inter-annual monthly micropollutant fluxes inputs (tributaries and the Upper Rhône River) compared to the output (Beaucaire station) claims for the presence of highly contaminated missing sources of micropollutants in the Rhône River watershed. Based on a SPM-flux-averaged micropollutant concentrations mass balance of the system and the estimates of the relative uncertainty of the missing sources concentration, we assessed their location within the Rhône River catchment. We assume that the potential missing sources of PAHs, PCBi and TME would be, respectively, the metropolitan areas, the alluvial margins of the Rhône River valley, and the unmonitored Cevenol tributaries.