LA MANGA, Spain — The Mar Menor, a saltwater lagoon on the coast of southeastern Spain, was long renowned for its natural beauty, drawing tourists and retirees to its pristine warm shallows and the area’s gentle Mediterranean climate.

But over the past few years, the idyllic lagoon has come under threat. Tons of dead fish have washed ashore as the once-crystalline waters became choked with algae.

Scientists are divided over whether climate change — causing excessive heat that reduces oxygen levels in water — is contributing to the problem. But they agree that nitrate-filled runoffs from fertilizers from nearby farms have heavily damaged the waters where oysters and sea-horses used to thrive. But farmers in the area have balked at shouldering the blame.

Hugo Morán, a senior official in the central government’s environment ministry, estimated that 80 percent of the water contamination resulted from the unchecked growth of agriculture. He also put some of the blame on local politicians, accusing them of long downplaying the contamination and proposing unviable remedies, such as channeling plenty of the lagoon’s waters into the Mediterranean Sea.

This would only create another victim, he said.

“To heal, you first have to recognize the illness,” he said. “But what we have heard, instead, are sporadic claims by the regional government of Murcia that the Mar Menor is doing better than ever.”

Similar problems have cropped up in other parts of the world recently. Pollution, including from nitrogen-based contaminants, has been blamed for accelerating the secretion of a slimy substance called mucilage that has clogged the Sea of Marmara in Turkey. And waste produced by a nearby electricity plan and oil refinery has damaged the giant Berre lagoon in southern France.

The area around the Mar Menor, with its fertile fields and temperate year-round climate, has proved irresistible to large-scale farms, which often use ecologically damaging nitrate fertilizers. Adding to the problems, there has been extensive tourism development on the narrow, 13-mile sandbank known as La Manga, or the Sleeve, that separates the Mar Menor from the Mediterranean.

Whoever is to blame, María Victoria Sánchez-Bravo Solla, a retired schoolteacher, has had enough.

When five tons of dead fish washed up in August near her house on the lagoon, she decided that she was ready to move. She called it “an environmental disaster that should put our politicians and all those who deny responsibility for allowing this to happen to shame.”

Such mass die-offs of fish have happened a few times over the past five years, and the stench of decomposing algae, which has turned the lagoon’s waters darker and murkier, is a further sign of the ecological crisis.

Local restaurants no longer serve Mar Menor seafood and commercial fishing crews now trawl in the nearby Mediterranean instead. Few residents would even consider taking a dip in the lagoon anymore.

As the problems have intensified, so has the blame game.

The conservative administration of the Murcia region says the Spanish central government in Madrid, currently a left-wing coalition, should do more to help. Madrid says the responsibility lies at the local level.

Miriam Pérez, who is responsible for the Mar Menor in the regional government, said she believes political rivalries are keeping the central government from doing more.

“I unfortunately do think that political colors matter,” she said.

She said the central government had done little to support her right-wing administration’s cleanup efforts — including removing about 7,000 metric tonnes of biomass — mostly decomposing seaweed — even after the region issued a decree in 2019 to protect the lagoon.

In August, when another wave of dead fish washed up, scientists noted that the water temperature had climbed significantly. But in September, the Spanish Institute of Oceanography published a report that rejected the idea that excessive summer heat helped kill the fish.

Scientists instead place much of the blame with farming. In 1979, a canal was opened to carry water from the Tagus — the longest river in the Iberian Peninsula — to southeastern Spain. The canal led to irrigation, which transformed Murcia into one of Europe’s farming powerhouses, producing lettuce, broccoli, artichokes, melons and more for export across the continent.

Agriculture represents 8.5 percent of the region’s gross domestic product and provides about 47,000 jobs, according to a study published last year by the University of Alcalá, near Madrid.

But the farmers around the Mar Menor have deflected the blame, saying that the contamination comes from water seeping into the lagoon from an aquifer in which toxic substances have accumulated over decades.

Vicente Carrión, president of the local branch of COAG, an agriculture union, said that farmers were now strictly using only the amount of fertilizers needed for plants to grow.

“We are getting blamed for what went on 40 years ago” when less scrutiny was placed on agricultural practices and the authorities’ emphasis was on taking advantage of the demand from across Europe, he said.

Adolfo García, director of Camposeven, an agriculture exporter that harvests about 1,500 acres of land in the region, said that most farmers had already switched to sustainable production methods. Laggards should get government incentives to invest in green technology rather than “stones thrown by people who have no knowledge of our modern irrigation systems,” he added.

“Even if we planted nothing in this area for the next 50 years, the aquifer would remain very polluted,” he said.

But Julia Martínez, who grew up in the region and is now a biologist and technical director at Fundación Nueva Cultura del Agua, an institute that specializes in water sustainability, said that the arguments about the aquifer were a red herring. She said at least 75 percent of the lagoon’s water contamination came from runoffs.

The impact of tourism — another giant contributor to the local economy — is another problem. The Mar Menor’s hotels and restaurants are concentrated along the sandy bar of La Manga, where dozens of apartment blocks were also built, many as holiday homes. Almost every inch of the strip is developed.

Mr. Morán, the environment secretary, acknowledged that the Mar Menor had suffered from an “open bar” approach in terms of awarding building permits. But he mostly blamed fertilizer runoff from farms.

The lagoon was proof that “one of the major problems of Europe is the contamination of its waters by nitrates,” he said.

Pedro Luengo Michel, a biologist who works for Ecologistas en Acción, a Spanish environmental organization, said the farming and tourist industries have broad influence, particularly at the local level where the conservative Popular Party has governed since 1995.

“We are confronting a very powerful farming lobby which our politicians depend on to stay in power,” Mr. Luengo Michel said.

Mr. Morán said that his central government planned to use 300 million euros, or about $350 million, from the European Union’s pandemic recovery fund to protect the Mar Menor’s natural habitat and waters. The plan includes replanting vegetation close to the shores, which can stop contaminated water flowing in from neighboring fields.

For some scientists, monitoring the deterioration of the lagoon has felt like a personal tragedy.

“I remember finding it stunning as a child that I could see the sand at the bottom without even noticing the water because the Mar Menor was so transparent,” said Ms. Martínez, the biologist.

“Now, we sadly have a green soup and I certainly have long stopped swimming in it.”