Estuaries, rias, fjords and lagoons (collectively called transitional waters, TW) are highly important ecosystems both for their high productivity but also as sites of urban and industrial development, supporting many major cities and ports. Increasingly they are accepted as transitional environments and in Europe this term has been given legal and management importance; indeed, in some cases this has led to decisions with high economic repercussions. We have thus revisited the fundamental properties and paradigms of these systems in the light of recent ecological theory. The analysis has produced a unifying approach to transitional waters, by adopting and expanding the concept of ecotone to whole ecosystems, rather than ecosystem boundaries. Furthermore we have addressed the paradoxes related to (1) the gradients concerning variability and stability in the system, (2) the biodiversity and ecosystem functioning, as well as (3) the response and resilience of the system to anthropogenic stressors. We conclude that the term Transitional Waters is not merely a legal convenience or that the TW are merely an interface, with positive and negative characteristics, but ecological systems in their own right.