Our nation's rivers, streams, and small bodies of water -- which have long been protected by the Clean Water Act -- are now in danger because of a series of misguided court decisions. Recent interpretations of the law suggest that many waters historically protected from pollution can now be polluted or destroyed without a permitting process to limit the environmental impact of discharges into the waters. This October 2008 issue paper discusses the particular danger of this change in interpretation in relation to the problem of nutrient pollution in the Mississippi River Basin. Pollution from the Mississippi contributes to the annual formation of an enormous "dead zone" in the Gulf of Mexico, an area where the bottom layer of water is so oxygen-depleted that most sea life cannot survive within it. This paper provides recommendations for reaffirming long-standing protections for our nation's waterways, including the wetlands and streams that play an important role in filtering pollution in the Mississippi River Basin.