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Nokoué Lagoon in the South of Benin is a large intermittent coastal water body in West Africa, which supports one of the largest inland fisheries of the region. The seasonal and interannual variability of its salinity was studied, based on 3 years of monthly surveys (Dec 2017 -Dec 2020. This dataset allows us to identify fine-scale salinity structures and to better understand the salinization/desalinization processes at seasonal scales. During the rainy season from May to November, under the influence of large freshwater inflows from the rivers on its northern shores, the lagoon desalinizes to a salinity of zero in October-November.During the dry season from December to April, under the effect of the ocean tide, Nokoué lagoon becomes progressively saltier, reaching typical salinities of ~25 in April. On average, the Nokoué lagoon is saltier in its southwestern part and fresher towards the river's mouths.Vertical salinity stratification is largest in December at the beginning of the main dry season.The lagoon displays a very marked interannual variation with mean surface (bottom, respectively) salinity of 25 (25) in April 2018 and 2020, respectively, against 16 (18) in April 2019. In the absence of river inflow data, a box model shows that the average salinity of the lagoon is very sensitive to small changes in river inflow (or discharge), with observed interannual differences in salinity induced by small variations of 10-15 m 3 s -1 in inflow during the dry season. During the salinization phase, the model suggests that ~30% of the seawater entering the lagoon during flood-tides remains trapped and enhances the Nokoué lagoon salinity. This model also indicates that a complete desalinization of the lagoon occurs for river inflow greater than ~50-60 m 3 s -1 . The general mixing time scale of the lagoon is of 30-40 days.

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