In Europe, the Water Framework Directive aims at reaching good ecological status for surface waterbodies by 2015. Consequently European countries have developed methods based on biological, hydromorphological and physico-chemical quality elements for the assessment and monitoring of rivers, lakes, coastal and transitional waters. In addition to the five ecological status classes (high, good, moderate, poor or bad) for each waterbody, the WFD requires that “estimates of the level of confidence and precision of the results provided by the monitoring programmes shall be given in the (monitoring) plan”. Such estimates are especially important to avoid misclassification of water bodies in their ecological assessment, which could, in extremis, lead to challenges to the final implementation of the Directive. Many factors will affect the final outcome of the assessment exercise, such as sampling design, year(s) of sampling, operator, etc. Therefore the impact of these factors on the assessment must be known and quantified. The European Framework project WISER is supporting the implementation of the WFD by testing and complementing existing assessment schemes, with a focus on the effects of uncertainty on classification strength, in order to make existing assessment methods more reliable and more defendable. The present work focuses on fish-based indicators for estuarine and lagoon (transitional waters in the WFD) quality. Changes in fish assemblages may not only reflect human impact but also several other sources of variability linked to sampling and natural parameters. This is especially true in transitional waters where natural abiotic variability is extremely high (Elliott and Quintino 2007). For reliable fish-based ecological status assessment, the natural sources of variability impacting fish assemblages need to be identified and their impact on fish metrics and fish indicators must be assessed and, if possible, reduced (Clarke and Hering 2006, Staniszewski et al. 2006). In this context, we focus on the variability sources potentially affecting fish metrics for transitional waters. Hence the present work represents the first step of a global uncertainty assessment with the following three main goals: - To give an overview of all factors that may affect the value of the most common WFD fish metrics in use for transitional waters and to identify the key sources of variability for these metrics. - To test the effect of these key sources of variability on individual fish metrics using a European dataset. - To indicate the general requirements of a sampling protocol that minimizes uncertainty for the fish-based assessment of transitional waters and to highlight main estuarine or lagoon features responsible for natural between estuaries or lagoon variability. - Finally, a method based on a Bayesian framework is proposed to objectively combine fish metrics in a multimetric indicator