Enforcement of federal environmental law is complex. Central to the efficacy of enforcement is the role of prosecutors and judges in exercising their discretion over which violations to prosecute and what sanctions to impose. In the context of the Clean Water Act (CWA), discretion is exercised in an institutional framework of marginal deterrence, criminal sanctions, broad prosecutorial discretion, and judicial discretion constrained by the Federal Sentencing Guidelines. After describing the CWA institutional framework for enforcement, a review of legal, economic, and criminal justice dimensions of exercising discretion is provided. It is concluded that while broad prosecutorial discretion is justified on economic efficiency grounds, extending criminal sanctions to outcomes lacking violator intent or control is likely to result in the overcriminalization of environmental law. Equally troubling, if judicial discretion is used to impose significant downward departures from the FSG, the trivialization of CWA enforcement is inevitable. Thus, overzealous prosecution runs the risk of creating overdeterrence and stripping criminal sanctions of their moral stigma, while lax criminal sanctioning undermines deterrence objectives while minimizing the importance of violating federal environmental law itself. Policy implications of recent sanctioning trends, as well as future research needs, are also explored.