Xochimilco is a network of ancient, man-made canals and floating islands in southern Mexico City – an area that was named a UNESCO World Heritage site in 1987. Today it’s known for its crowds of tourists and brightly painted party boats. But Lucio Usobiaga is focused on something else here: ancient farming practices. “Farming organically is the best way to preserve the chinampas ,” he says of the islands. Mr. Usobiaga co-founded a nongovernmental organization, Yolcan, in 2011 to preserve and spread this kind of farming in Xochimilco. In doing so, he also aims to improve the livelihoods of smallholders and to bring local, organic produce to those living in Mexico City, one of the biggest metropolises in the world. Noe Coquis Zaldivar and his father have served as local liaisons for Yolcan, and Mr. Coquis has noted changes in the community since the NGO’s arrival. “Before we were using agrochemicals,” he says. “It was a challenge to see if we could grow new things.... There are more people expressing interest in joining the network of producers; there’s curiosity around what’s happening here.”

Lucio Usobiaga has childhood memories of going to Xochimilco, a network of ancient, man-made canals and floating islands in southern Mexico City. When he thinks back, he can hear the blasting mariachi music, smell the grilled corn, and see the garbage floating in the waterways.

Today, the area is still known for its crowds of tourists and brightly painted party boats, but Mr. Usobiaga’s associations with Xochimilco have changed. Sitting on the bench of a green wooden boat, known as a trajinera, he’s surrounded on a recent morning by calm glassy waters, white egrets soaring into flight, and the resurgence of ancient farming practices.

“Farming organically is the best way to preserve the chinampas,” Usobiaga says of the islands created in the Valley of Mexico that were incorporated into a larger network of waterways by the Aztecs and later the Spanish.

Usobiaga co-founded a nongovernmental organization, Yolcan, in 2011 to preserve and spread these farming practices in Xochimilco. In doing so, he also aims to improve the livelihoods of smallholders and bring organic, local produce to those living in Mexico City – one of the biggest metropolises in the world.

“The idea from the beginning was to make [Yolcan] about ecology, economy, and connecting peasant farmers with consumers” in a megacity, Usobiaga says.

This morning the trajinera pulls up to one of the floating islands, and Usobiaga hops off. He’s giving the owner of a cafe and a handful of other visitors a tour, showing them how the food that Yolcan provides to some of the top chefs in the city is grown. The food is also distributed via weekly farm boxes to more than 150 individuals, families, and schools.

The group carefully crosses a short bridge. Usobiaga points to the gravel and bamboo in the water below – a natural filtration system that Yolcan worked on with university students from a local engineering school. It allows farmers to purify the polluted water and use it for irrigation.

Yolcan, which means “land of origin” in Nahuatl, has introduced new vegetables and varieties to the chinampas in an effort to keep the soil healthy and producing year-round. Mostly young men have partnered with Yolcan, pulling up orange and pink beets, piling up leaves of chard, and cutting off heads of purple cauliflower.

The area was named a UNESCO World Heritage site in 1987, protecting it from development. But in recent decades, it’s become more common to find the islands rented out for soccer matches or birthday parties than tilled by chinamperos, as farmers here are known.

Getting farmers on board

Persuading local farmers to get on board with Yolcan’s vision was a challenge initially.

“At the beginning they weren’t interested because they didn’t trust that what we were doing was going to work,” Usobiaga says. The way most farmers had learned to survive was to produce one crop in bulk in order to sell it to the largest wholesale market in Latin America, Central de Abastos. Usobiaga and his partner, Antonio Murad, who focuses largely on bookkeeping, encouraged people to move away from monoculture and stop using chemicals. They also decided they could set an example.

“We changed our strategy and said, ‘We’ll do it ourselves and hope they’ll start coming,’ ” Usobiaga recalls.

Ginnette Riquelme Lucio Usobiaga (r.) works with two farmers in Mexico City’s Xochimilco to deliver vegetables to a restaurant.

Key to this was finding a local partner who bought into the idea of making small but important changes. Noe Coquis Zaldivar and his father served as that bridge for Yolcan. Mr. Coquis was working at a nearby park when Usobiaga approached him.

At first he turned Usobiaga down, as he was busy with farming his own land and working at the park. But then he started thinking about the goal of helping locals reclaim the chinampero tradition and making a decent living in the process.

“It’s sad people here don’t want to dedicate themselves to the land,” he says. “They go to the city to find work, and their priority is to leave the fields.”

Since Yolcan arrived, Coquis says he’s noted changes in the community. “Before we were using agrochemicals,” he says. “It was a challenge to see if we could grow new things.... There are more people expressing interest in joining the network of producers; there’s curiosity around what’s happening here.”

Five families in Xochimilco are working full time with Yolcan, out of roughly 30 farming here. Some will never join the project simply because they are able to make more through the agrochemical approach.

Yolcan buys what the project’s farmers produce. The price Yolcan pays depends on what is grown as well as on the season and market price, Usobiaga says.

“The farmers have the commitment to produce the food organically and sell what they’ve committed to only to us,” he says. “In exchange, we give them all the advice, workshops, technical assistance, seeds, ingredients for fertilizers, and we follow through on our commitment to buy everything we’ve agreed to.”

A different life before farming

Usobiaga didn’t grow up farming; in fact, he grew up in a very different environment. “Where I come from, the social background is private schools and you have your road already paved out for you,” he says. “Agriculture is never on the table. Never. Neither is philosophy,” he says of the subject he studied in university.

He sees a direct link between his studies and agriculture, though. “Working with farmers and the land has given me a way to put some of those [philosophy] ideas into place,” he says. “For example, Aristotle says ‘being’ is said or thought about in many ways. That has taught me to see agriculture in its many different meanings and as a tool for ecology, health, food, and social justice.”

It’s not just farmers reaping the benefits of Yolcan’s work. Nearly three days a week one of Mexico’s top chefs, Eduardo García, wakes up before dawn to take a trajinera out to the chinampas and pick out the produce he’ll serve in his restaurants.

Having access to locally grown, organic food “changes everything for me as a chef,” says Mr. García, who sources from a handful of organic suppliers. When he opened the restaurant Maximo Bistrot in 2011, he estimates that 80 percent of his produce came from the city’s wholesale market. Today, thanks in large part to Yolcan, it’s closer to 80 percent organic.

“For my restaurants, it’s important because I feel that it helps me in a way to do less work, because [the food] is already pure. It tastes like it should taste,” he says.

Farm boxes with daikon radishes

Yolcan is also trying to connect farmers and consumers. “In Mexico, only the rich people and the farmers can eat right,” Usobiaga says. “What happens to all these people in between?” he asks.

The farm boxes are a recent development. Although they’re getting “easier and easier” to sell, they’re sometimes met with confusion and complaints.

“The boxes are full of things people aren’t familiar with,” he says, noting daikon radishes and rutabaga. “We need to work on delivery, making lettuce arrive crisper, not having any insects or bugs in the vegetables,” he acknowledges.

Mexico “is still in that phase where it’s cool to say that you eat organic or you support local farmers, but it’s not really true yet,” he says. “But we’re closing the link between farmers and consumers, and that can make all the difference.”

Three other groups involved in ecology

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• EcoLogic Development Fund works with rural and indigenous peoples to protect tropical ecosystems in Central America and Mexico. Take action: Aid efforts in Honduras’s Pico Bonito National Park.

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• Osa Conservation applies scientific and other expertise to safeguarding the biodiversity of the Osa Peninsula in Costa Rica. Take action: Give money to the organization’s sea turtle conservation program.

• Let Kids Be Kids is an advocate for disadvantaged individuals, as well as animal species that are at risk. Take action: Support indigenous peoples.