“A sum can be put right: but only by going back till you find the error and working it afresh from that point, never by simply going on.” C.S Lewis. Factory farm runoff is a growing concern affecting people, animals, and the ecosystem as a whole. The best way to combat this problem may not directly be to try and think of safer ways to dispose of the toxic waste, or even attempt to eliminate the issues of factory farm runoff by simply going on.
Attacking the problem from an empathetic standpoint and from a root of the issue may be the only way to change how factory farms are run. The main products produced from factory farms are meat, milk, and eggs. Here the animals are exposed to terrible and hazardous living situations. The animals are packed into confined spaces, causing stress and anxiety. In a high stress and compact animal environment, fighting between animals is commonplace. Imagine being packed into a farmhouse the size of a football field with hundreds of other people for weeks on end. 
When fighting breaks out there are few solutions. The most common being the removal of beaks, teeth, tails, wings, or anything that can be used as a weapon. This is also a common practice for any animals that are forced into cannibalism. However, the worst part about this is that it is too expensive to use pain killers so the farm animals must endure this pain. Many of which die from shock; most commonly piglets after having their teeth or tails removed.
In these stables there is little room for exercise which is the farmers intent. When the animals are not able to move around, their bones and muscles do not fully develop creating more fatty meat. Air quality is also extremely poor, which leads to nearly unlivable conditions. In such a confined space, bacteria and disease are so common that the only way to control this is by using pesticides and antibiotics. The FDA reported that in 2009, 80% of all antibiotics administered were to livestock. Many of which are closely tied to antibiotics used to treat illness in humans. The consequence of this leads to immunities and higher healthcare related costs.
Factory farms creating these inhumane and even deadly living conditions for farm animals is completely unethical. Animal rights should be considered in these extreme conditions. Eliminating the treatment that many of these farm animals endure would be a giant step towards controlling the factory farm runoff issue and the multitude of effects that ensue. The only way to stop a leak is to cut it off at the source, and factory farm runoff is the leak. It is our job to find the source and fix it.
http://www.fao.org/docrep/009/a0158e/a0158e00.HTM
http://foodandwater.wpengine.netdna-cdn.com/wp-content/uploads/2010/11/FactoryFarmNation-web.pdf
