This study aims to identify and to quantify the main external sources of nitrogen for a coastal lagoon in Mediterranean context. The paper first reviews the existing methods for quantifying nitrogen loads, coming from the main sources: rainfall, sea exchanges, domestic and industrial effluents, urban area runoff, rivers and aquifer. When possible, the accuracy of the different methods is discussed for annual, event-based or daily estimates. Moreover, an original mathematical model is proposed here for estimating the river loads: POL model is an event-based model for nitrogen loads calculation on small intermittent rivers. Nitrogen loads are then quantified on the specific example of the Thau lagoon. The annual nitrogen budget is presented for the year 1998–1999 and for a storm event (11 November 1999). Rainfall loads are estimated using amounts and concentrations that were measured on the lagoon catchment. Sea–lagoon exchanges are extrapolated from a previous study conducted between 1994 and 1996. Local water authorities’ database is used to estimate nitrogen loads in domestic effluents. Nitrogen loads associated to urban runoff are estimated using an empirical model, since no data are available. Groundwater nitrogen inputs are quantified from the monthly monitoring (September 1998–August 1999) of the three main karstic springs flowing into the lagoon. Nitrogen loads coming from the rivers are evaluated using POL model. The results show that, on an annual basis, the rivers and the aquifer bring two-thirds of the nitrogen loads to the lagoon. Urban runoff has a negligible impact. The estimate of sea–lagoon exchanges has a low accuracy, mostly due to the poor quality of the data. During the storm event, the main part of the nitrogen loads is brought by the rivers but rainfall has also an important contribution. The daily basis comparison shows the regular contribution of the sewage treatment works in the nitrogen loads tend to become predominant during the summer season.