The Water Framework Directive requires all Member States to achieve good ecological quality status for all waters (e.g., transitional waters). For that purpose, Member States must assess water bodies based on information on the Biological Quality Elements listed for each of them (e.g., benthic macroinvertebrates). However, the production of such a quality status classification (high, good, moderate, poor, bad) requires high reference conditions (associated with the absence of, or very low, human pressure) against which the deviation of the samples to be assessed can be measured. In transitional waters, upper stretches have seldom been included in monitoring activities, resulting in very little knowledge of mesohaline and oligohaline areas, which means further difficulty when defining the required reference conditions for these zones.