Ecotoxicological data are highly important for risk assessment processes and are used for deriving environmental quality criteria, which are enacted for assuring the good quality of waters, soils or sediments and achieving desirable environmental quality objectives. Therefore, it is of significant importance the evaluation of the reliability of available data for analysing their possible use in the aforementioned processes. The thorough analysis of currently available frameworks for the assessment of ecotoxicological data has led to the identification of significant flaws but at the same time various opportunities for improvement. In this context, a new methodology, based on Multi-Criteria Decision Analysis (MCDA) techniques, has been developed with the aim of analysing the reliability and relevance of ecotoxicological data (which are produced through laboratory biotests for individual effects), in a transparent quantitative way, through the use of expert knowledge, multiple criteria and fuzzy logic. The proposed methodology can be used for the production of weighted Species Sensitivity Weighted Distributions (SSWD), as a component of the ecological risk assessment of chemicals in aquatic systems. The MCDA aggregation methodology is described in detail and demonstrated through examples in the article and the hierarchically structured framework that is used for the evaluation and classification of ecotoxicological data is shortly discussed. The methodology is demonstrated for the aquatic compartment but it can be easily tailored to other environmental compartments (soil, air, sediments).