The human mediated transfer of aquatic organisms and pathogens via shipping, specifically with ballast water, is a continuing global threat to biodiversity, human health and economic values. In February 2004, as a result of long-term effort of the International Maritime Organization (IMO), the United Nations body which deals with shipping, the International Convention for the Control and Management of Ships’ Ballast Water and Sediments (BWM Convention) was adopted by the international community setting global standards. In the absence of efficient Ballast Water Treatment Systems (BWTS) on existing ships, Ballast Water Exchange (BWE) is currently the only available method approved by IMO. However, BWE has serious limitations that make it biologically inefficient and often impractical under certain conditions. A key question is whether all ships should be requested to conduct BWE (i.e., blanket approach) or whether it is more appropriate that port states determine BWE requirements on a ship-to-ship basis (i.e., selective approach) supported by a decision support system based on risk assessment? In this paper BWE in the framework of the BWM Convention is discussed. The applicability and effectiveness of BWE is studied and suggestions are given for an effective ballast water management approach, including options for a decision support system, in Europe.