SAN JOSE, Costa Rica — An outcry over national sovereignty. Camouflaged armed officers policing the border. Costa Rica is not acting like its usual tranquil self lately.

The country is angry, charging neighboring Nicaragua with dumping river sediment and clearing forest in protected wetlands that belong to Costa Rica.

After sending an official complaint to Nicaragua last week, Costa Rica is waiting for the government of President Daniel Ortega to explain itself. The accusations arise from what was supposed to be a harmless Nicaraguan government-run dredging project in the Rio San Juan, Nicaragua’s 120-mile-long river.

“We had a guarantee,” Carlos Roverssi, Costa Rica’s vice foreign minister, told reporters Tuesday. “They were going to conduct only a small dredging that wouldn’t affect Costa Rican territory. But what happened is a violation of our national sovereignty … that changes the circumstances.”

Starting in Lake Nicaragua, the San Juan runs much of its 120 miles along a natural border with Costa Rica, and rather uncomfortably so. For more than a century, the countries have sparred over navigation and fishing rights. Those disputes were mostly settled in a July 2009 case in the International Court of Justice in The Hague, Netherlands.

Now the San Juan finds its way back to the middle of a fray, this time with Ortega’s dredging project that began this month. He plans to remove river sediment that makes it hard to navigate the San Juan’s waters. He also hopes that deepening the river will redirect the water back up to Nicaragua, after heavy sedimentation had driven the flow into Costa Rican territory for the last 20-mile stretch toward the Caribbean.

The Nicaraguan president put a fellow Sandinista revolutionary hero, Eden Pastora, in charge of the project. He’s been at the head of what some Costa Rican columnists are calling a “tragicomedy.”

Pastora, known during the 1979 revolution as “Comandante Cero,” has been charged with picking a fight with the country that once served as his guerrilla hideout.

Farmers on the Costa Rican side of the river allege that a group of 10 or so armed men led by Pastora invaded their land and harassed workers and killed livestock.

Then came the environmental violations.

Costa Rica’s security minister, Jose Maria Tijerino, revealed photos that show the river sediment being dumped on Costa Rican territory.

Then Tijerino accused Pastora of cutting down trees on a sliver of Costa Rican land in what the security chief said was an apparent attempt to build an 300-foot-long canal that would link the San Juan and the Laguna de los Portillos, both Nicaraguan-owned bodies of water.

When GlobalPost asked Tijerino whether Costa Rica had at any point given permission for the sediment dumping or the tree felling, he responded: “Never. We could never authorize such a thing. It’s an intrusion on national territory.”

Last week, Costa Rica began daily flyovers of the region and deployed police to guard its side of the river. Officials declined to specify how many police, but press reports put the number at 150, relaying that some of the officers are in camouflage and carrying M-16s and M-60s — an odd site in a country that abolished its army more than 60 years ago.

As of Tuesday, Costa Rican authorities said Managua had not responded to their complaint.

Beyond the security threat, scientists are concerned about what deforestation and dumping will do to the environment.

Freddy Pacheco, a biologist at Costa Rica’s National University, accused Nicaragua of violating the Convention on Biological Diversity, which Costa Rica and Nicaragua both signed.

“If you look at the fauna, that area has tapirs, manatees, jaguars, the tropical gar fish, the famous green macaw and more than 300 other bird species, at least 30 mammal species and dozens of reptiles and amphibians, insects and crustaceans,” he said.

“I’m not just talking about Costa Rica,” said Pacheco. “I’m talking about both countries. Nature has no borders. There, it’s only a biological corridor.”

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