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The palaeoenvironment of a former coastal lagoon in the south eastern Iberian Peninsula (San Rafael, Almeria, Spain) were inferred from one core analyzed for particulate organic matter content (POM) together with its C/N, delta(13)C, delta(15)N to depict the biogeochemical record from the Late Glacial to the Holocene. The results, complemented by previously reported pollen assemblages, indicate the appearance of a freshwater lagoon at 7300 B.P. (uncalibrated (14)C age), its salinization at 6200 B.P. and its disappearance at 4400 B.P. The period of existence of the lagoon coincided with a period of wetter conditions as inferred from terrestrial vegetation. The lagoon’s salinization was not related to a decrease in precipitation but to a stronger maritime influence since there were no parallel changes in terrestrial vegetation. Salinization caused an increase in delta(13)C, associated with a higher relative presence of C(4) plants, and an increase in delta(15)N, due to a decrease in plant N demand. The late period of the lagoon, from about 5100 to 4400 B.P., shows a progressive drying and salinization not detected in isotopes but reflected in a decrease in POM, and in the pollen records. Increases in delta(15)N were related to increases in salinity within the lagoon, and are indicative of a more open N cycle, because the absence of changes in terrestrial vegetation rules out changes in the catchment area as the cause for changes in delta(15)N.