Water Framework Directive (WFD) statutory authorities and stakeholders in Ireland are now challenged with the issue of how the proposed programmes of measures in the newly required River Basin Management Plans – designed to protect and restore good ecology by reverting as closely as possible back to natural conditions – are to be implemented in a way that concurrently complies with other existing and emerging intersecting European Union legislation, such as the Floods Directive (FD). The WFD is driven largely by ecological considerations, whereas the FD and other legislation are more geared towards protecting physical property and mitigating public safety risks. Thus many of the same waterbodies, especially heavily modified waterbodies, arguably have somewhat competing policy objectives put upon them. This paper explores the means by which Ireland might best achieve the highest degrees of cost effectiveness, economic efficiency and institutional durability in pursuing the common and overarching objective of the WFD and FD – to ensure Irish waterways are put to their highest valued uses.