I feel I have to weigh in on Don's side here. I have practiced environmental law for about 20 years, both as an attorney with an environmental advocacy group, and as in house counsel for a railroad. My employers have both sued and been sued under the very provisions of the Clean Water Act (and their state equivalents) that are mentioned here. The bottom line is that no one is allowed to put anything into a water of the United States without a permit. As Peggy and Don's messages have pointed out, not all of the regional offices of EPA agree completely, but I put that down more to differences in philosophy as to how to enforce the statutes, not in their base interpretation.
To those of you who see local sewage plants as the real problem, not overboard discharge of marine toilets: I agree with you that the sewage plants have a greater overall impact on water quality, but should be careful what you wish for. The grand majority of treatment plant issues relate to the fact that (at least here in the northeast) are hooked up to what are known as "Combined Sewer Overflow" (CSO) systems. This means that the street sewers are hooke up to the sanitary sewers, and they all go to the treatment plant before discharge to the local water body. However, when it rains, the treatment plant capacity cannot handle the extra flow from the street sewers; this leads to the system automatically letting the street sewers dump into the water body without treatment. I think we all have stories of finding disgusting crap floating in the water or on the beaches after a storm; well, that's where it comes from. Not to mention the dog, bird and other animal wastes that get washed into the sewers during a storm that greatly affect water quality. Those of you out there who say we should address these issues before picking on us poor boaters should carefully consider the costs of "fixing" this problem. There is really only one way to fix the problem: increase treatment capacity at the sewage plants so they can handle the flow of the storm sewers during a rainstorm. This is enormously expensive. It has taken us over thirty years (since the passage of the original Clean Water Act) and billions in investments to get us this far, and will take similar time, resources and effort to take us those final steps. In the meantime, I don't think the existing no-discharge laws for boats are unreasonable. After all, I see too many knuckleheads on the water who don't know and don't care about basic safety laws, and I sincerely doubt that those types would have a problem discharging their toilets wherever it is most convenient for them. I am all for making it very difficult for that crew to ruin my afternoon.