Runoff directly into the water, whether the bay or fresh water, is a major problem. The feces and urine have a number of pathogens dangerous to humans. Pigs are to be no closer than 50 feet from any water but as seen here and other images, they are often directly on the water because it is easy to wash to waste from the pigs into the water.
The FSM EPA has a constant battle for compliance for the correct placement of pigs and the impact to human health and welfare.