[I]n 2000 the National Water Quality Inventory reported that agricultural nonpoint source pollution is the leading source of water quality impacts on surveyed rivers and lakes, the second largest source of impairments to wetlands and a major contributor to contamination of surveyed estuaries and ground water[.] Agriculture activities that cause NPS pollution include poorly located or managed animal feeding operations, overgrazing, and improper, excessive or poorly timed application of pesticides, irrigation water and fertilizer. . . .
Pollutants that result from farming and ranching include sediment, nutrients, pathogens, pesticides, metals and salts. Using management practices that are adapted to local conditions can minimize impacts from agricultural activities on surface water and ground water. Many practices designed to reduce pollution also increase productivity and save farmers and ranchers money in the long run. . . . Farmers apply nutrients such as phosphorus, nitrogen and potassium in the form of chemical fertilizers, manure and sludge. When these sources exceed plant needs, or are applied at the wrong time, nutrients can wash into aquatic ecosystems. There they can cause algae blooms, which can ruin swimming and boating opportunities, create foul taste and odor in drinking water, and kill fish by removing oxygen from the water. High concentrations of nitrate in drinking water can cause methemoglobinemia, a potentially fatal disease in infants, also known as blue baby syndrome. To combat nutrient losses, farmers can implement nutrient management plans that help maintain high yields and save money on fertilizers.
The farmers, by and large, aren't breaking the law. The Clean Water Act and the regulations promulgated under it, contain broad exemptions for agricultural operations. The main federal environmental regulations governing pesticides and fertilizers are those under food quality regulations designed to protected harvested fruits and vegetables from posing harm to people who eat them.
Current regulations aren't designed to meaningfully protect farm workers or the environment. For example, from a food safety perspective, excessive pesticide or fertilizer application that is later washed away in runoff doesn't matter at all, while failure to protect food from pests could be a concern, so there is a regulatory bias in that encouraged sending agricultural chemicals into runoff.
The main reason that farmers were exempted from most provisions of the Clean Water Act was out of a concern that it would mostly impact small businesses that would lack the economic resources to comply. A related reason was that in the late 1970s, the options for reducing pollution from agriculture were less understood than the options for reducing pollution from industry and power plants.
The world has changed in thirty years. The vast majority of farm production comes from very large operations which are capable of implementing suitably crafted environmental regulations without going bankrupt. And, as the article above notes, there are now well understood ways to reduce agricultural pollution that actually reduce a farmer's expenses.
Rising oil prices tend to increase the prices of fertilizer and pesticides, many of which either have petroleum as a component in their production, or are energy intensive to produce, transport and apply. Environmental concerns are just one more part of a chorus of concerns about the prevailing practices in conventional American agriculture (mostly not shared by organic agriculture).
While I am not convinced that organic agriculture provides health benefits to food consumers that are very significant, it is becoming increasingly clear that the time has come for a widespread shift towards organic agricultural practices (even if not with the same rigor), for both economic and environmental reasons.
This should probably come, in part, through federal environmental regulation of agriculture, a change which would probably pose the least compliance burden not necessary to achieve environmental goals, if it was offered as a single, industry specific environmental law, rather than as piecement amendments and regulatory changes in a variety of existing environmental laws and regulations that contain exemptions for agriculture now.