This paper reviews the characteristics, benefits, and drawbacks of agricultural ditches and wetlands, as well as strategies for applying agricultural best management practices (BMPs) at the watershed scale for improving water quality. This synthesis focuses on the Great Lakes Region and the Mississippi River Basin in the United States, and specifically crop production systems in watersheds with subsurface drainage. The USDA Natural Resources Conservation Service (NRCS) has developed conservation practice standards for open channels and wetlands, which mitigate nutrient and sediment loading to surface water bodies from agricultural lands. Practices that use agricultural ditches to improve water quality, such as the two-stage ditch, have emerged in the last two decades and are starting to see a greater application in the region. Using wetlands as water treatment systems has a long history in a range of settings and over the past several decades is seeing more widespread application in agriculture. Water quality and watershed models are increasingly used to develop watershed strategies for reducing nutrient exports with agricultural BMPs. Models are also helpful in evaluating combinations of practices from the farm scale to the watershed scale. Application and limitations of several models commonly used in these regions of the United States are discussed. Finally, successful conservation strategies at the watershed scale must consider the human dimensions of watershed management, and we summarize the literature in this region on farmer perceptions and adoption of practices.