In Thau coastal lagoon, phosphate concentrations have decreased by 89% from 1971 to 1994. The present relatively long term (over 25 years) study compares changes in the contribution of point (PS) and non-point sources (NPS) total phosphorus (P) loads. The analysis of the distribution of the sources in comparison with the changes in the phosphate concentrations in the Thau lagoon aims to point out their relative impact in order to create a sustainable management plan for this system. This is needed, firstly because water quality supports shellfish farming, which is the main economical activity of the basin. Secondly, because the population is planned to increase by 40% between 1995 and 2020 thus leading to an increase of urban pressures. PS P loads, represented by discharges by wastewater treatment plants, have increased by 143% while NPS P loads, both represented by export from lands and loads from non-connected population, have decreased by 64%. Despite important changes in land-use by an exceptional decrease of vineyards areas (−12.5%), domestic effluents main contribute (>60%) to both PS and NPS P loads and seem to be more implicated in the decrease of phosphate concentrations in the Thau lagoon, probably because of the different phosphorus forms engaged.