Large scale farms often do not properly dispose of animal waste such as manure and methane. Animals produce 3x as much manure as humans. This often makes it's way into waterways and then a cholera epidemic breaks out.

Pesticides and hormones also present a threat to the environment.
Large scale farms also require large amounts of water to feed crops and livestock taken from finite sources of groundwater.
Large scale farms are also very fossil fuel reliant, adding greenhouse gasses to the atmosphere.
While animals in large scale farms are given less food, produces less manure, and reaches market faster than ever before, the environment impact has only increased. This is because small farms of the past achieved a balance in the natural productivity of the land, while modern large farms are very unbalanced.
Water Stress:
87% of water usage in the United states is for Agriculture. It takes countless gallons of water to irrigate crops, then countless more for the livestock on top of those crops. many large scale farms are located in dry environments, putting large amounts of stress on the local environment because of the farm's water demands. many groundwater and drinking water in the US is being outstripped.
The best solution to this problem is to educate people about it. Water stress is not as well known as other environmental threats such as climate change or colony collapse. As people become more educated about this problem, they will alter their lifestyles to take on more water-friendly aspects, because I really don't think life with major water shortages will be very fun. Except for the cars.

http://www.circleofblue.org/waternews/2010/world/experts-name-the-top-19-solutions-to-the-global-freshwater-crisis/
Nice GIF
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