Eutrophication is one of the largest threats to aquatic ecosystems in the world. Mar Menor hypersaline lagoon is an example of a coastal lake under eutrophication risk due excessive nutrients loads, nitrogenand phosphorus, that came from its catchment area including urban and agricultural sources. Regular loads and punctual loads during flooding events produce algae blooms that can reduce significantly water oxygen content and cause massive mortalities, such as have been occurred in last years. A daily algae growth model (Mmag) was developed to better understand the processes and determine keyelements that require further analysis in next years, such as phosphorus water-sediment interchange orthe deep plants effect in the entire ecosystem and in the algae growth. The analysis strategy developed can be applied in other wetlands around the world. In the Mar Menor both nitrogen and phosphorus havehigh relevance depending on period of the year and the phosphorus legacy. An integrated set of measures is required to reduce mean chlorophyll to levels under 1 or 0.5 µgChla/l that can make Mar Menor more robust and resilient.