An understanding of the ecological functioning of an aquatic continuum on a multi-regional scale relies on the ability to collect suitable descriptive information. Here, the deterministic Seneque/Riverstrahler model, linking biogeochemistry with the constraints set by geomorphology and anthropogenic activities, was fully implemented to study the Seine, Somme, and Scheldt Rivers. Reasonable agreement was found between calculated and observed nutrient fluxes for both seasonal and inter-annual variations along the networks. Nutrient budgets underline: i) a clear partition of diffuse and point sources with respect to the specific activities of the watersheds, ii) the importance of riparian retention, responsible for 25-50% of nitrogen retention, iii) the role played by benthic processes, resulting in the retention of up to 45% of the phosphorus and 35% of the silica entering the river systems. Nutrient ratios confirmed that fluxes to the Eastern Southern Bight of the North Sea are imbalanced, supporting the potential for undesirable algal blooms.