• Mono-culture:

[By] the 1990s, only six varieties of corn accounted for 46 percent of the crop, nine varieties of wheat made up half of the wheat crop, and two types of peas made up 96 percent of the pea crop. Reflecting the global success of fast food, more than half the world's potato acreage is now planted with one variety of potato: the Russet Burbank favored by McDonalds. "[ http://www.portaec.net/library/food/the_downside_of_industrial_agriculture.html ]

• dependence:

on finite non-renewable fossil fuel energy resources, as an input in farm mechanization (equipment, machinery), for food processing and transportation, and as an input in agricultural chemicals.

An increase in energy prices can be expected to result in increase in food prices

An increase in price/reduction in output could also arise from phosphate outage. Finite phosphate reserves are currently a key input into chemical fertilizer for industrial agriculture.

• Demands of continuous growth • Demands of scale • Ethical abominations:

Economies of scale require pesticides, fertilizers, machinery, antibiotics, etc.'

To produce as much meat, eggs, or milk at the lowest possible cost, "confined animal feeding operations" or "intensive livestock operations", can hold up to hundreds of thousands of animals, often to never see the light of day or move beyond their own excrement.  

Food and water is supplied in place, and artificial methods are employed to improve production, such as antimicrobial agents and growth hormones, physical restraints and crippling to prevent interaction or flight (e.g. for chickens, individual cages  and de-beaking to prevent pecking at cages). Weight gain is encouraged by the provision of plentiful supplies of food to animals breed for weight gain.

• standardization 

The need for standardized seeds, feed, pesticides, fertilizers, drugs, etc.

• Waste concentrations:

Scale leads to dangerous concentrations of wastes such as manure,

• Nutrient-depleted soils:

Our foods have become less nutritious because our soils have fewer nutrients

• Increased health risks from pesticides

• Increased ozone pollution via methane byproducts of animals

• Global warming from heavy use of fossil fuels

• Environmental and social costs • surface and groundwater polluted with animal waste • Damage to fisheries

Industrial agriculture uses huge amounts of water, energy, and industrial chemicals; increasing pollution in the arable land, usable water and atmosphere. Herbicides, insecticides, fertilizers, and animal waste products are accumulating in ground and surface waters. Moseley, W.G. 2011. "Make farming energy efficient." Atlanta Journal-Constitution. June 3. pg. 15A.

A study done for the US. Office of Technology Assessment conducted by the UC Davis Macrosocial Accounting Project concluded that industrial agriculture is associated with substantial deterioration of human living conditions in nearby rural communities. Macrosocial Accounting Project, Dept. of Applied Behavioral Sciences, Univ. of California, Davis, CA

But not just nearby rural communities: "Many of the negative effects of industrial agriculture are remote from fields and farms. Nitrogen compounds from the Midwest, for example, travel down the Mississippi to degrade coastal fisheries in the Gulf of Mexico. But other adverse effects are showing up within agricultural production systems -- for example, the rapidly developing resistance among pests is rendering our arsenal of herbicides and insecticides increasingly ineffective." Union of Concerned Scientists article The Costs and Benefits of Industrial Agriculture ( March 2001)

Chemicals used in industrial agriculture, as well as the practice of monoculture, have also been implicated in Colony Collapse Disorder which has led to a collapse in bee populations. Agricultural production is highly dependent on bee pollination to pollinate many varieties of plants, fruits and vegetables. Colony Collapse Disorder

The US Environmental Protection Agency (EPA) has identified certain animal feeding operations as point source polluters of groundwater, subject to special anti-pollution regulation. Sweeten, John et al. "Fact Sheet #1: A Brief History and Background of the EPA CAFO Rule". MidWest Plan Service, Iowa State University, July 2003.

In 17 states in the U.S., isolated cases of groundwater contamination has been linked to CAFOs.[http://sustainableagriculture.net/our-work/conservation-environment/clean-water-act/] For example, the ten million hogs in North Carolina generate 19 million tons of waste per year.[http://www.edf.org/news/north-carolinas-hog-waste-lagoons-public-health-time-bomb] The U.S. federal government acknowledges the waste disposal issue and requires that animal waste be stored in lagoons. These lagoons can be as large as 7.5 acres (30,000 m2). Lagoons not protected with an impermeable liner can leak waste into groundwater under some conditions, as can runoff from manure spread back onto fields as fertilizer in the case of an unforeseen heavy rainfall. A lagoon that burst in 1995 released 25 million gallons of nitrous sludge in North Carolina's New River. The spill allegedly killed eight to ten million fish.[Orlando, Laura. McFarms Go Wild, Dollars and Sense, July/August 1998, cited in Scully, Matthew. Dominion, St. Martin's Griffin, p. 257.]
 

References:

The Downside of Industrial Agriculture

http://en.wikipedia.org/wiki/Industrial_agriculture