1. Transitional waters, described as critical transition zones because of their position at terrestrial, freshwater and marine interfaces, provide essential goods and services to the biosphere including human populations. These ecotones face increasing human influence mainly due to population density increase in coastal areas. 2. Transitional water bodies have, to date, received little attention in the development of ecological status indicators, this is a critical deficiency when trying to meet the Water Framework Directive objective of all significant water bodies achieving good ecological status by the year 2015. 3. In order to assess changes in transitional water communities many taxonomic-based indicators have already been proposed but there are a number of concerns for their use such as taxonomic classification difficulties, their unsuitability for multi-site comparisons and their inconsistent relationships with disturbance or stress. 4. Alternative methods based on body size, abundance distribution among functional groups, functional diversity and productivity descriptors are proposed. These methods offer the opportunity to compare sites with different taxonomic compositions and allow derivation of indicators related to ecological status of communities under scrutiny. 5. Finally, the suitability of these taxonomic-free descriptors to provide relevant information for each of the four main biotic compartments in coastal lagoons is discussed. The use of biomass distribution among functional groups for fish, benthos and macrophyte and to use body-size distribution for benthos and plankton is proposed. Copyright (c) 2006 John Wiley and Sons, Ltd.