Farming probably has the biggest impact over the largest land/water scale use of all of human activities. Growing food for people requires more land alteration than any other activity mankind undertakes in its efforts to survive and thrive. Many believe the Dust Bowl period in the US was caused by farming practices which left the soils vulnerable to wind erosion factors. There is some truth to that idea, but the dust bowl itself was caused by an abnormal and lengthy drought period. Were conditions to return to that drought state, there would be another dust bowl episode, probably on a much grander scale due to the increased pressures and changes to the land, that has occured since this time period.
Soil degradation is having an impact on the conservation efforts regarding watersheds and wetlands. As runoff does occur, the chemicals used on farms congregate in the lowlands or run off into the streams and rivers causing pollution issues. Another issue is using marginal lands for food production which increase the amount of chemicals needed to produce a crop. This in turn impacts how much of these chemicals are pushed into the waters by the natural processes of weather.
Agriculture is the largest single non-point source of water pollutants including sediments, salts, fertilizers (nitrates and phosphorus), pesticides, and manures. Pesticides are commonly found in groundwater beneath agricultural areas; they are widespread in the nation's surface waters. Eutrophication and "dead zones" due to nutrient runoff affect many rivers, lakes, and oceans.
Other environmental ills include over 400 insects and mite pests and more than 70 fungal pathogens that have become resistant to one or more pesticides; stresses on pollinator and other beneficial species through pesticide use; loss of wetlands and wildlife habitat; and reduced genetic diversity due to reliance on genetic uniformity in most crops and livestock breeds.
This is not to say that methods of farming couldnt be implemented to reduce the risk of a dust bowl event. This is not to say that utilizing more organic methods within farming practices themselves wouldnt help reduce the losses suffered in the soils themselves by our habits of agriculture. And this involves a move towards 'sustainable agriculture' methods and practices.