This study aims at determining how the boron signal of the Seine River evolved in terms of concentration and isotopic signatures over eighteen years (1994–95 and 2006–12) and if boron isotopes can reliably trace anthropogenic inputs over time. In the anthropised Seine River watershed, boron is widely released by human activities, and even if boron concentrations ([B]) are below the potability limit, our study confirms the potential of boron isotopes (δ11B) to trace urban anthropogenic contaminations. Between 1994 and 2012, [B] have decreased across the anthropised part of the Seine River basin (and by a factor of two in Paris) while δ11B has increased. This means either that urban inputs have been reduced or that the boron signature of urban inputs has changed over time. Both hypotheses are in agreement with the decrease of perborate consumption in Europe over 15 years and are not mutually exclusive. Results of a thorough analysis of urban effluents from the sewage network of Paris conurbation that are in fine released to the Seine River suggest a shift of the urban δ11B from −10‰ in 1994 to 1.5 ± 2.0‰ in 2012, in agreement with our second hypothesis. We attribute this change to the removal of perborates from detergents rather than to the modernisation of wastewater treatment network, because it does not significantly impact the wastewater boron signatures. Eighteen years after the first assessment and despite the decreased use of perborates, geochemical and isotopic mass budgets confirm, that boron in the Seine River basin is mainly released from urban activities (60–100%), especially in Paris and the downstream part of the basin. Contrastingly, in headwaters and/or tributaries with low urbanisation, the relative boron input to river from agricultural practices and rains increased, up to 10% and by 10 to 30%, respectively.