In this paper we examine briefly the provisions of two European acts establishing a criminal penalty system for discharges of polluting substances in waters under the jurisdiction of EU Member State. Although the two European legislative acts were adopted in 2005, the conducted research represents a novelty, and it can be useful both to theorists, practitioners in the field, and to the European legislator. Essential contribution to the field, is to examine the documents adopted at EU level, as well as critical opinions formulated, completed and the need to supplement or taking another piece of legislation, given the new changes in the structure of crime in the area, and the need for effective preventive measures. Also, the paper highlights the need for increased specific activities of judicial cooperation in criminal matters between Member States, by adopting effective legislation, including the territorial jurisdiction and resolve operational conflicts of competence Also, the paper highlights the need for increased specific activities of judicial cooperation in criminal matters between Member States, by adopting effective legislation, including the territorial jurisdiction and hence the operative resolving conflicts of jurisdiction arising between Member States or between a Member State or a state not a member of the European Union.