The Soil and Water Assessment Tool (SWAT model, 2001 Version) has been applied to the Than lagoon catchment area in order to simulate water discharges and nutrient inputs into the lagoon over a 10 years period (1989-1999), and to provide routing inflows to a previously developed lagoon ecosystem model. The watershed model has been calibrated and validated using measured data available for the two main rivers. The results indicate that the mean annual nitrogen inputs into the Thau lagoon is 117 +/- 57 tons y(-1), with the two main rivers, contributing for 80% of total annual nitrogen export. The variations of outputs to the lagoon are nonetheless important from 1 year to another. Due to the local agricultural practices and a reduced in-stream natural depuration, point sources seem to be the main factor affecting the fresh water quality. The coupling with the lagoon model allowed to estimate the impact of those terrestrial inputs on the lagoon nitrogen cycling and primary productivity. Influence of river discharges makes itself felt essentially near the river outlets. The northern bordure of the lagoon is then characterised by highly variable dissolved inorganic nitrogen concentrations, especially during flood events, while more stable and lower concentrations were simulated in the southern part of the lagoon. Simulated chlorophyll a ranged 1-15 mu g l(-1), with maximums in March. Mean annual phytoplankton production was 364 +/- 142 gC m(-2). The simulations showed that maximum annual productions are due to macrophytes (up to 1300 gC m(-2) y(-1)), but at the whole lagoon scale, annual phytoplankton production resulted greater. From our results it also appeared that the greatest part of primary producers nitrogen requirements is satisfied by nutrient regeneration within the lagoon.