This article assesses the long-term hydro-sedimentary and ecological consequences of the urban pressure around Paris over the last 3000 years on the Merantaise river. Using a geoarchaeological approach combining sedimentological, geochemical, palynological and geophysical investigations enabled us to identify the transformations of the hydrosystem and to discuss the consequences of the different types of pressure and to put the role of biophysical and historical legacies into perspective with respect to contemporary dynamics. Using two study sites, one a former pond (Merancis), the other a former mill site (Ors mill), nine cores, two auger holes and four trenches dug in the valley floor and two electrical resistivity tomography (ERT) profiles, it was possible to reconstruct the geometry of the sedimentary deposits. Chronostratigraphy was based on 41 radiocarbon dates and the history of vegetation and anthropogenic activities was reconstructed from 42 pollen samples and non-pollen palynomorphs collected from the former pond site. Despite the expansion of wetlands in the valley bottom, the pollen data revealed strong agropastoral activities and cereal growing in the Iron Age and up until the end of the Middle Ages. For the first time, sedimentological data associated with pollen data revealed hemp retting activities from c. 675 CE. From the Late Middle Ages onwards, water management led to the creation of two ponds to feed water mills. Despite the persistence of wetlands, this study highlights the early onset of anthropogenic modifications and in particular, the start of organic pollution and eutrophication in the Early Middle Ages, attesting to early eutrophication of water quality and aquatic environments resulting from the transformation of agropastoral practices and hydraulic pressure around the largest European city during the last 1500 years, well before the inset of urban sprawl in the watershed.