The effect-directed analysis (EDA) methodology is an important component in site-specific risk assessment of contaminated aquatic systems, but improves its relevance in assessment strategies when confirmed on ecosystem level. Several approaches are available to confirm the ecological relevance of EDA results, but just a few studies exist, directly linking EDA processes with field studies in the aquatic environment. In this chapter, approaches on different assessment levels ranging from molecular responses to integrated community analysis are summarised in a multiple line of evidence approach to illustrate their potential use in EDA-confirmation procedures. Biomarkers were identified to have the potential to bridge bioassay-identified chemicals from EDA studies to effects in indigenous organisms on a mechanistic level. In situ bioassays use reference organisms to directly link exposure to EDA-identified chemicals to site-specific effects on organisms at realistic exposure conditions. For the sites of investigation, in-depth information on chemical concentrations and site-specific community data may be available from monitoring programs. These data can be used to confirm the relevance of EDA-identified chemicals by linking their concentrations to community-level effects. The SPEAR-index directly links changes in macroinvertebrate communities to site-specific contaminants. Multivariate statistical tools and prognostic modelling based on the TU-approach or on ms-PAF modelling may reveal correlations of EDA-identified chemicals and provide prognosis on potential impacts on the ecological status. Next to the principles and examples of the suggested approaches constraints and challenges are discussed, when aiming to link the methodology of EDA with ecological-based site assessment.