It all comes down to selective enforcement. The Clean Water Act is Federal therefore it applies to everyone (Jersey is correct). Some may qualify for exemptions, others will simply live in areas where enforcement is lacking. Just like all other federal environmental laws including CERCLA, RCRA, etc., the states may assume primary enforcement authority by promulgating their own regulations provided that the state law is "equal to or more stringent than the federal law". The frustrating thing is that some people can ignore the regulations and not be punished, while others are denied permits or spend $$$ acquiring and maintaining their permits.
I've worked for both state and federal agencies and have been an environmental consultant for over 15-years and have seen hundreds of examples of selective enforcement. In an earlier post I said that it depends on which state you live in, that is not correct, it depends on which state, county and township. States like New Jersey, California, New York and Michigan have the tightest environmental enforcement in the nation.
If you live in an area where you can just put in a pond without a permit, consider yourself lucky but it may still be a violation. I know many people in rural townships in Michigan who have done just that, while I have spent five years and a lot of time and money for my permits. There would definitely not be any ponds on my property if I were not in the environmental business, did not know the permitting process well and could not do all the work myself.
Jersey, you are also right about having knowledge of the requirements. There is an ignorance clause standard in the penalty section of the regulations. Fines will be larger for those who have previous knowledge prior to committing a violation. Another reason why, I couldn't take a chance with my project. It could have cost me everything plus my career.
It's just a matter of time until enforcement hits the frontier. I'm not sure if pushing the issue through politicians would help or just increase enforcement actions. I tend to think it would be the latter. Scientific study on this issue will not show that the installation of ponds protects the nation's water supply (actually the contrary is probably true). My best advice is to buy an existing pond or buy property where you can put in a pond without a major headache (others have given this advice).
Let's face it, the Pond Boss forum is a small group of voters with little or no political clout. Let's say for sake of argument that an organized group was able to get the federal government's attention. From EPA's perspective, they would be obligated to find out why the Clean Water Act was not being enforced in certain areas and could threaten to pull federal funding from state programs. The result would not be positive for many potential pond builders but may result in more consistent enforcement.