The spatial distribution of silicate, ammonium, nitrate, nitrite, phosphate, chlorophyll a and dissolved oxygen in Óbidos lagoon was obtained by surveying five sites in eight campaigns, between October 2004 and October 2006. A confined inner branch of the lagoon showed higher availability of ammonium (1.2–81 μmol l⁻¹), phosphate (1.9–17 μmol l⁻¹), silicate (0.85–86 μmol l⁻¹) and chlorophyll a (0.30–18 μg l⁻¹) than other sites (0.47–25 μmol l⁻¹, 0.10–3.9 μmol l⁻¹, 0.47–25 μmol l⁻¹, 0.25–11 μg l⁻¹, respectively). According to several trophic classification tools, that branch is considered eutrophic to polytrophic, emphasising its deteriorated conditions, while the rest of the lagoon is of better quality. In autumn/winter nutrients were inversely correlated to salinity (r>0.93) reflecting the freshwater inputs enriched in nitrogen and phosphorous compounds to the inner branch. In warmer periods, dissolved oxygen concentrations dropped during the night, and sediments of the branch become an important source of ammonium and phosphate. The low DIN:P ratio (median=10) obtained in the branch, which suggests an excess of phosphate, that increased in warmer periods and changed the limiting nutrient in the entire lagoon. These results emphasize the spatial heterogeneity of water quality in Óbidos lagoon, its seasonal variability, and the importance of recognising these distributions before defining homogenous water body on the scope of Water Framework Directive.