The law was written targeted at large commercial ocean ships with ballasts to prevent the transport of aquatic nuisance species into non-native waters. The idea was that these nuisance species would hitch a ride in the ships and when ballast water was discharged, these species would be introduced where they aren't welcome. The EPA wrote in an exemption for recreational boats like yours and mine preventing us from being negatively affected by this regulation. That all changed when the EPA was sued and the judge ended up overturning the exemption when the EPA lost the suit. It forced the EPA to comply and institute a permit program leaving boaters like you and I to pay up.
The Clean Boat Act of 2008 has been adjusted to correct all of this and to prevent boaters like us from being required to pay for a permit to discharge water from our boats. It appears to have gone through Congress with success and is awaiting a siggy by the President. All is right with the world again.
For 34 years the federal Environmental Protection Agency (EPA) has exempted discharges from recreational boats from the Clean Water Act permit system. Regretfully, a fall 2006 U.S. District Court ruling cancelled this permit exemption. EPA is now required by the court decision to develop and implement by September 30, 2008 a national permit system for ALL vessels in the United States for a variety of normal operational discharges1
So you see, this is all thanks to a court ruling and not an attempt by the EPA to regulate some more or charge us money. I just want to make that very clear seeing as how anglers might get a little jumpy over anything viewed as "environmental protection."
You can read more about all of this in the following links.
1. "EPA Discharge Permit Requirement for Recreational Boats." Federal Alerts, 19 March, 2008. BoatU.S. Government Affairs. 30 July, 2008. < http://www.boatus.com/gov/fed_alert.asp >.