At the northern end there are salt flats, which include a wetland of international importance. This area is preserved as a natural park administered by the regional government: the  (‘San Pedro del Pinatar salt flats and sand beaches’). The microbes that live in this coastal lagoon have been recently described.
The islets and the few coastal places without permanent human constructions are a protected landscape: the  (‘Mar Menor open areas and islands’).
In 1994 the Mar Menor was included on the Ramsar Convention list for the conservation and sustainable utilisation of wetlands. 
The Mar Menor is also part of a Specially Protected Area of Mediterranean Importance and is a Special Protection Area (ZEPA in Spanish) for bird life.
In July 2016 pollution was reportedly so severe as to render the area close to ecological collapse, following 18 years of neglected warnings. The public prosecutors office is investigating allegations of negligence against the relevant authorities, which are governed by the conservative Peoples Party
In May 2017 all beaches of the Mar Menor were stripped of their Blue Flag status as a result of the polluted condition of the Mar Menor in 2016.
In October 2019 the pollution entering after floods in September led to thousands of dead fish lining the beaches, having suffocated due to a lack of oxygen. Intensive farming in surrounding areas leads to high levels of nitrates, ammonium and phosphates from fertilizers being washed into the lagoon, causing eutrophication, an excessive growth of algae and bacteria that deprives the water of oxygen.
A similar event occurred in August 2021, with four to five tons of dead fish being removed from the lagoon within a week. Shortly thereafter, a large demonstration took place, with 70,000 people surrounding the entire lagoon on August 28, 2021.