The Mar Menor (SE Spain), the largest hypersaline coastal lagoon of the Mediterranean basin, suffers a severe eutrophication crisis due to the nutrients that receives from the Campo de Cartagena watershed, mainly nitrate from intensive agriculture. This paper updates the state of the art in relation with nutrient discharges to the Mar Menor, and summarizes results from different tested Nature-Based Solution (NBS). Specifically, we show i) results from a pilot plant with woodchip bioreactors for nitrate-enriched brine denitrification, and ii) the first results obtained in a pilot plant with bioreactors and constructed wetlands for treatment of agricultural drainage water and leachates, as well as other effluents. Nutrient discharges to the lagoon are highly variable and occur via drainage network, drains, stormwater pipes, direct groundwater discharges from the Quaternary aquifer, and others. For instance, between January 2017 and January 2018 measured daily superficial discharge (floods excluded) ofN-NO3 − amounted from 119 kg d−1 to 1084 kg d−1. Estimations subsurface discharges ranged 815 to 3836 kg N-NO3 − d−1 in 2018–2020. Field studies in coastal wetlands (e.g. inflow ≈20–30 mg N-NO3 − L−1, removal ≈80–90%) and results from pilot plants with bioreactors (e.g. inflow ≈30–40 mg N-NO3 − L−1, removal ≈90–95%) and constructed wetlands (e.g. inflow ≈30–40 mg N-NO3 − L−1, removal ≈60–70%), showed the good performance of these systems for nutrient retention. Four strategies are considered for reducing nutrient inputs into the Mar Menor, which include a combination of nature-based solutions and best management practices. (i) Reducing the leaching of nitrate to the aquifer and export of nutrients and sediments following heavy rains by improving fertilization, and irrigation routines, and soil conservation measures in the agricultural fields. (ii) Development of effective and scalable tools for denitrification of nitrate-rich brine produced by onfarm desalination plants. (iii) Capture and treatment of polluted water discharged to the Mar Menor via hydrologic networks, subsurface flow, drainage ditches, and others. (iv) Preservation and restoration of coastal wetlands.