Based on the GRAFS method of biogeochemical accounting for nitrogen (N), phosphorus (P) and carbon (C) fluxes through crop, grassland, livestock and human consumption, a full description of the structure and main functioning features of the French agro-food system was obtained from 1850 to the present at the scale of 33 agricultural regions. For the period since 1970, this description was compared with the results of an agronomic reconstitution of the cropping systems of the Seine watershed based on agricultural census and detailed enquiries about farming practices at the scale of small agricultural regions (the ARSeine database), which were then used as input to an agronomical model (STICS) calculating yields, and the dynamics of N and C. STICS was then coupled with a hydrogeological model (MODCOU), so that the entire modelling chain can thus highlight the high temporal inertia of both soil organic matter pool and aquifers. GRAFS and ARSeine revealed that the agriculture of the North of France is currently characterised by a high degree of territorial openness, specialisation and disconnection between crop and livestock farming, food consumption and production. This situation is the result of a historical trajectory starting in the middle of the nineteenth century, when agricultural systems based on mixed crop and livestock farming with a high level of autonomy were dominant. The major transition occurred only after World War II and the implementation of the Common Agricultural Policy and led, within only a few decades, to a situation where industrial fertilisers largely replaced manure and where livestock farming activities were concentrated either in the Eastern margins of the watershed in residual mixed farming areas or in specialised animal production zones of the Great West. A second turning point occurred around the 1990s when regulatory measures were taken to partly correct the environmental damage caused by the preceding regime, yet without in-depth change of its logic of specialisation and intensification. Agricultural soil biogeochemistry (C sequestration, nitrate losses, P accumulation, etc.) responds, with a long delay, to these long-term structural changes. The same is true for the hydrosystem and most of its different compartments (vadose zone, aquifers, riparian zones), so that the relationship between the diffuse sources of nutrients (or pesticides) and the agricultural practices is not immediate and is strongly influenced by legacies from the past structure and practices of the agricultural system. This has strong implications regarding the possible futures of the Seine basin agriculture.