If you eat meat, the odds are high that you’ve enjoyed a meal made from an animal raised on a factory farm (also known as a CAFO). According to the USDA, 2% of U.S. livestock facilities raise an estimated 40% of all farm animals. This means that pigs, chickens and cows are concentrated in a small number of very large farms. But even if you’re a vegetarian, the health and environmental repercussions of these facilities may affect you. In his book Animal Factory, journalist David Kirby explores the problems of factory farms, from untreated animal waste to polluted waterways. Kirby talks to TIME about large-scale industrial farming, the lack of government oversight and the terrible fate of a North Carolina river.

What exactly is a factory farm?
The industrial model for animal food production first started with the poultry industry. In the 1930s and ’40s, large companies got into the farming business. The companies hire farmers to grow the animals for them. The farmers typically don’t own the animals — the companies do. It’s almost like a sharecropping system. The company tells them exactly how to build the farm, what to grow and what to feed. They manage everything right down to what temperature the barn should be and what day the animals are going to be picked up for slaughter. The farmer can’t even eat his or her own animals. People who grow chickens for Perdue in Maryland have to go down to the market and buy Perdue at the store.

We collectively refer to these facilities as factory farms, but that’s not an official name. The government designation is CAFO, which stands for Concentrated Animal Feeding Operation. Basically, it’s any farm that has 1,000 animal units or more. A beef cow is an animal unit. These animals are kept in pens their entire lives. They’re never outside. They never breathe fresh air. They never see the sun.

What are the health and environmental hazards of CAFOs?
For one, you’re often no longer feeding animals what they’re genetically designed to eat. CAFO cows eat a diet of milled grains, corn and soybeans, when they are supposed to eat grass. The food isn’t natural because they very often put growth hormones and antibiotics in it. That becomes a problem when you put that manure on the ground.

And the fact that there are thousands of animals packed into one farm is also a problem.
Oh, definitely. There are simply too many animals in too small of a place. In a traditional farm, a sustainable farm, you grow both crops and animals. There is a pasture, and you have a certain number of animals per acre. But when you have 2,000 cows per acre instead of two, you have a problem. You can’t fit them in a pasture — you fit them in a building. You can’t grow enough crops to feed them — you have to ship in their feed. You don’t have enough land to absorb their waste. It has nowhere to go.

So what happens to it?
The manure is liquefied. It gets flushed out into an open lagoon, where it is stored until farmers can use it on what few crops they do grow. There’s just so much of it, though. I’ve seen it sprayed into waterways and creeks. These lagoons filled with waste have been known to seep, leak, rupture and overtop. This stuff is untreated, by the way. We would never allow big, open cesspools of untreated human waste to just sit out on the ground near people’s homes and schools. And yet because it’s agriculture, the rules are different.

You write at length about North Carolina’s Neuse River. What happened there?
Hundreds of massive pig farms came into North Carolina in the 1990s. In Animal Factory, I tell the story of Rick Dove, a former Marine who retired and bought a fishing boat. One day he noticed the fish were dying in really weird ways. First there were the algae blooms. Algae creates oxygen during the day through photosynthesis and expels carbon dioxide at night. When that happens, there’s literally no oxygen in the water. Everything comes crawling up to the shore in the shallowest part of the river, trying to pump water through their gills. By the morning, they’re all dead. Everything — shrimp, crab, little fish called menhaden, eels, bass. People call it a “fish jubilee,” ’cause they can just wade into the river and pick up free food.

Soon after this started happening, Rick Dove noticed the menhaden fish were developing round red circles on their flanks. They’d go into what was called a “death spiral.” They just start swimming into little circles and just die. Nobody knew what was causing this. Pretty soon after that, the fishermen, including Rick and his son, noticed they were getting round red sores on their skin in the parts that touched the water. Then they’d get very disoriented. Fishermen would forget where they lived or where they’d docked their boats. Rick started to do some research. One day he read in a science magazine about pfiesteria, this very odd plankton that emits toxins that stun a fish so it can suck the fish’s blood. That’s what the lesions were. But the toxin also gets in the air, and that’s why fishermen were getting disoriented.