The federal government usurped power over navigable water in the early 1800's by distorting the Commerce Clause listed in the Enumerated Powers (Article1, Section 8) of the Constitution, which says:
"To regulate Commerce with foreign Nations, and among the several States, and with the Indian Tribes;"
The Commerce Clause has been stretched far beyond federal regulations over trade transactions and taxes; it now extends to federal authority over the means of commerce (trucks, roads, telephones, etc) and almost anything that crosses state lines (industry, fish, pollution, etc). This is an illogical abuse of the Constitution, but it fits the plan for centralized control.
Because water affects human health directly, government regulations over water are appropriate to PROTECT human health and property (but no more and no less than that). The states are the obvious choice for regulating water because they answer more directly to the People who live there, instead of a central federal one-size-fits-all policy.
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