The hut on Maua beach, a sleepy fishing community on the north edge of Rio de Janeiro’s Guanabara Bay, is almost unnoticeable. The turquoise doors of the dirty, whitewashed shack are bolted, and a small frosted porthole reveals nothing of the building’s purpose.

In Mage, an impoverished town of 250,000, far from the glamour and wealth of Rio’s beaches and skyscrapers, wooden fishing boats line the shore and stray dogs wander about aimlessly. The faded letters above the door read Ahomar – in English, the Association of the Men and Women of the Sea.

Meanwhile, 46 miles away, oil executives and government officials last month gathered at a luxury hotel for a multibillion-dollar auction for the rights to the massive Libra oil field, 140 miles off Rio’s coast.

For industry watchers, the story was the deal struck by a consortium of Brazilian and foreign companies for the 12 billion barrels of reserves, paying £4.27bn in signing fees alone. But for human rights campaigners, the real story lies back in Mage – where a battle is being fought for the soul of Guanabara Bay.

It is a battle that Alexandre Anderson de Souza, 43, knows too well. The seaman has his home in Mage and has moored his boat off the beach for years. Like thousands of others, his livelihood depends on the sealife of the beautiful, 19-mile bay, at the end of which sits the city of Rio. Once, the bay had healthy mangroves, clean beaches and a teeming ecosystem. But decades of reckless development led to its pollution, and a disastrous leak in 2000 saw more than a million litres of crude spew into the bay from a pipeline owned by the Brazilian state-owned energy giant, Petrobras.

The leak destroyed many of the mangroves; 13 years later, despite efforts to clean up the bay, they have yet to return. For Mr de Souza and his friends, nothing was the same after the leak. Whereas before they could land hundreds of pounds of fish in a day, afterwards they could only land a handful – and the catch was often contaminated by oil.

When it was clear that Petrobras was intent on building a second massive refinery, Comperj, costing £224m and promising thousands of jobs to the local construction industry, on the bay, Mr de Souza says the fisherman had to fight – or lose their livelihoods.

“It would be the end of us,” he said. “We need the sea to eat and to support our families. In the 1990s, there were 23,000 families fishing the bay. Now there are fewer than 5,000.”

With his friends, in 2007 he formed Ahomar, which now represents about 2,000 men and women who fish for a living in the shadow of Sugarloaf Mountain. Their active resistance included anchoring their boats to stop construction of new pipelines, and using their nets to prevent large ships from passing through the bay.

Soon after that, he says, the violence started. Mr de Souza – who as the group’s leader claims he has survived six attempts to kill him – says he was first shot at by two men near the pipeline works in May 2009.

Weeks later, the organisation’s former treasurer, Paulo Cesar dos Santos Souza, was shot in the head five times in front of his wife and children. Before he was killed, his assailants are claimed to have dragged him out of his house, beaten him and questioned him about Ahomar activities.

In January the following year, fisherman Marcio Amaro was killed. Previously, he is said to have filed a formal complaint about what he claimed were illegally armed men at the construction site.

Mr de Souza was given police protection, but the attempts on his life continued. In July 2010, he returned home with his wife to find two armed men waiting outside his house. He called the police, and a shoot-out ensued.

In June 2012, the Rio+20 summit brought dozens of heads of state to Rio to discuss environmental policies. Just as the summit was drawing to a close, two leaders of the association, Almir Nogueira de Amorim and Joao Luiz Telles Penetra, went out fishing in the bay and did not return alive.

Mr Penetra’s body washed up at a shipyard days later, reportedly with his arms and legs tied with rope in the foetal position. Mr de Amorin’s body was found in the same state: he was tied to his boat and had bruises on his neck.

After these killings, Mr de Souza was forced out of Mage. “He had been under police protection at home for three years, but it just became too dangerous for him to remain there,” said Renata Neder, Amnesty International’s human rights adviser.

“The security guards who worked on the construction sites are very often the same men that are linked to the militias who control the area, and to the police. It is difficult for him to be safe in his own home.”

Earlier this month, there were break-ins at Mr de Souza’s home and Ahomar’s offices. Both were vandalised and property, including computer equipment, was stolen. “They are trying to drive us from our bay, but I never want to stop this fight. I never want to give in,” Mr de Souza said.

His family of seven spent months being put up in hotels by Brazil’s human rights protection programme and are now in hiding in an apartment elsewhere in the state.

Speaking to The Independent on Sunday from his hideaway, he said he was determined to continue the fight: “We want to return to our home, our residence, our city, to go back to Ahomar to continue our fight. We cannot give up. It is our community. I need to return.”

He blames groups tied to subcontractors on the pipelines for the violence. Approximately 15,000 people have been working at the site for around 20 consortia. In total, 200,000 direct and indirect jobs are expected to be created at Comperj.

A spokesman for Petrobras, one of the world’s largest companies, with revenues last year of £89bn, said: “Petrobras repudiates any threats to the fishermen and categorically reaffirms that it has had no involvement with the cases.”

He added that the company “maintains a constant dialogue with these stakeholders and others in the communities. Additionally, all Petrobras projects strictly follow the provisions of environmental licences.

“Petrobras has supported various environmental and social initiatives in Guanabara Bay, such as Projeto Mova Brasil [which supports adult literacy], and others.”

Ms Neder, of Amnesty, added: “We believe Alexandre is now safe, but we have two main demands.

“We want him to be able to return to Mage to continue his work. And we want all of the murders and threats against Ahomar to be investigated properly – which we do not believe they have been.”

Caitriona Rice, protection coordinator for the Americas for NGO Frontline Defenders, said: “Even when investigations are carried out they tend to take a very long time; convictions are rare and the identification of the intellectual authors of attacks on human rights defenders are even rarer.”

Mr de Souza declined to talk last week about the deaths of his friends. But previously he has spoken about how their loss has driven him on: “They were drowned by the water that flows from the very river we are trying to save, the environment we are trying to preserve.

“They kill us and we bury our friends. When we bury them, a little bit of ourselves goes with them. But we will not be driven out of our homes on Guanabara Bay.

“The choice is simple – either we impose our will and survive – or we leave things as they are and use our boats as firewood to cook our last meal on the beach.”