During the past three decades, there has been an increasing interest in the field of ecotoxicology for development of effect-based monitoring tools (EBMTs) including in vitro tests, biomarkers and whole organism bioassays. This interest is due to the practical application of EBMTs in the surveillance of the quality of water and aquatic ecosystems (ICES, 2008). Within this framework, these ecotoxicological tools seem to offer numerous potential advantages, as they allow one to take into account the cumulative impact of the whole contaminants present in the field, and the bio-available and active fractions of toxicants as well as their degradation bioaccumulation, biotransformation (Lam and Gray, 2003; Hecker and Hollert, 2009). Hence, they are often seen as complementary tools to conventional environmental monitoring approaches, mostly based on the measurement of a predefined list of chemical substances in various aquatic compartments (water, sediments and biota) and the analyses of indices of biological integrity (OSPAR 2004). Due to these research activities, several core EBMTs (SGIMC, 2011) are now well characterised and may be directly used to assess the quality of the aquatic environment under a European consensus (Table 1; Sanchez and Porcher, 2009; Lyons et al., 2010). However, if EBMTs are widely used in research studies and provide, at geographically and temporally limited scales, data on ecotoxicological status of water bodies, few applications of EBMTs are currently implemented in regulatory environmental monitoring programs.