Back in 2005, a federal court in California held that the US EPA’s rule exempting ballast water discharges from regulation (the rule is found at 40 C.F.R. 122.3(a)) was not consistent with the Clean Water Act and directed the EPA to revise its rules to regulate ballast water discharges. See Northwest Environmental Advocates v. U.S. EPA, No. C 03-05760 SI (N.D. Cal. Mar. 30, 2005). In September 2006, the same court issued an order revoking the EPA exemption as of September 30, 2008. While the EPA is appealing the decision, if the appeal is not decided before the exemption is revoked on September 30, 2008, then any ships discharging ballast water will be violating the CWA and subject to enforcement lawsuits. To avoid that, the EPA has proposed a general permit to cover all commercial and large recreational vessels that incorporates the Coast Guard’s mandatory ballast water management and exchange standards and creates supplemental ballast water requirements for vessels that carry ballast water. The EPA has also proposed a general permit to cover discharges from all recreational boats. The EPA will be taking public comments on the proposed general permits for 45 days. For more information on the proposed general permits and public comment opportunities (including a public meeting in Chicago on June 26), see the EPA’s Vessel Discharges webpage.
Update - Here are some of the most legally substantive public comments by environmental groups, states, and regional organizations on the EPA's proposed general permit for ballast water discharges:
Download Northwest Environmental Advocates ballast water permit comments (submitted on behalf many national and regional environmental organizations)
Download NWF ballast water permit comments (submitted on behalf of several national and Great Lakes regional environmental organizations)