This opinion paper focuses on the role of eco-toxicological tools in the assessment of possible impacts of emerging contaminants on the aquatic ecosystem, hence, on human health. Indeed, organic trace pollutants present in raw and treated wastewater are the pivot targets: a multidisciplinary approach allows defining the basic principles for managing this issue, from setting a proper monitoring campaign up to evaluating the optimal process treatment. Giving hints on trace pollutants fate and behaviour, attention is focused on the choice of the bioassay(s), by analysing the meaning of possible biological answers. Data interpretation and exploitation are detailed with the final goal of providing criteria in order to be able to select the best targeted treatment options. The manuscript deals with conventional and innovative analytical approaches for assessing toxicity, by reviewing laboratory and field assays; illustrative real scale and laboratory applications integrate and exemplify the proposed approach.