A fully coupled, two-dimensional hydrodynamic and reactive-transport model of C, N, O 2 and Si along a river-estuarinecoastal zone system is presented. It is applied to the Scheldt continuum, a macrotidal environment strongly affected by anthropogenic perturbations. The model extends from the upper tidal river and its tributaries to the southern Bight of the North Sea. Five dynamically linked nested grids are used, with a spatial resolution progressively increasing from 33 m to 2.7 km. The biogeochemical reaction network consists of aerobic degradation, nitrification, denitrification, phytoplankton growth and mortality, as well as reaeration. Diagnostic simulations of a typical summer situation in the early 1990s are compared to field data taken from the OMES database (>300 samples per variable). Results demonstrate that the process rates in the tidal river are very high and far larger than in the saline estuary, with maximum nitrification rates in the water column up to 70 mM N day − 1 , and maximum aerobic respiration and denitrification up to 70 and 40 mM C day − 1 , respectively. Phytoplankton production is about one order of magnitude lower, a result which confirms the dominance of heterotrophic processes in this system. The influence of secondary and tertiary wastewater treatment in the catchment is then assessed. Results show a significant decrease of organic matter and ammonium concentrations above Antwerp, which in turn leads to a partial restoration of oxygen levels. The model also predicts a reduction of denitrification rates, which locally results in a 4-fold increase of the nitrate concentration. Mass budgets for carbon, nitrogen and oxygen are established for the saline estuary (km 0 to 100) and for the tidal river network (km 100 to 160). Three scenarios, corresponding to the situation in the early 1990s, the years 2000 and the situation expected in 2010 are considered. They show that the tidal river and the estuary contribute almost equally to the overall biogeochemical cycling of these elements, despite the very different water volumes involved. For the simulated periods, the large decrease in nitrogen input (> 55%) expected between 1990 and 2010 will not lead to a significant decrease of N export to the coastal zone during the summer period.