Either way, the effects are severe. For instance, water quality across the country is threatened by phosphorus and nitrogen, two nutrients present in animal wastes. In excessive amounts, nutrients often cause an explosion of algae that robs water of oxygen, killing aquatic life. One toxic microorganism, Pfiesteria piscicida, has been implicated in the death of fish in coastal waters in North Carolina.

The Environmental Protection Agency reported that "Since 1995, an additional one billion fish have been killed from manure runoff in estuaries and coastal areas in North Carolina, and the Maryland and Virginia tributaries leading into the Chesapeake Bay. These deaths can be directly related to the 10 million hogs currently being raised in North Carolina and the 620 million chickens on the Eastern Shore of the Chesapeake Bay."

Manure can also contain traces of salt and heavy metals, which can end up in bodies of water and accumulate in the sediment, concentrating as they move up the food chain. And lagoons not only pollute groundwater; they also deplete it. Many factory farms use groundwater for cleaning, cooling and providing drinking water.

Meat production also significantly increases global warming. Cow farms produce millions of tons of carbon dioxide and methane per year, the two major greenhouse gases that together account for more than 90 percent of U.S. greenhouse emissions, substantially contributing to “global scorching.”

Meat-based diets contribute disproportionately to global and local environmental problems including climate change, rainforest destruction, and other habitat loss, species extinction, soil erosion, air and water pollution, and desertification.