Aquatic ecosystems are continuously contaminated by agricultural and industrial sources. Although the consequences of this pollution are gradually becoming visible, their potential impacts on aquatic ecosystems are poorly known, particularly regarding the risk of bioaccumulation in different trophic levels. To establish a causality relationship between bioaccumulation and disease, experiments on biotic matrices must be performed. In this context, a multi-residue method for the analysis of 35 emerging pollutants in three benthic invertebrates (Potamopyrgus antipodarum, Gammarus fossarum, and Chironomus riparius) has been developed. Because the variation in response of each individual must be taken into account in ecotoxicological studies, the entire analytical chain was miniaturised, thereby reducing the required sample size to a minimum of one individual and scaling the method accordingly. A new extraction strategy based on a modified, optimised and miniaturised "QuEChERS" approach is reported. The procedure involves salting out liquid-liquid extraction of approximately 10-20 mg of matrix followed by nano-liquid chromatography-nano electospray ionisation coupled with tandem mass spectrometry. The validated analytical procedure exhibited recoveries between 40 and 98% for all the target compounds and enabled the determination of pollutants on an individual scale in the ng g(-1) concentration. The method was subsequently applied to determine the levels of target analytes in several encaged organisms which were exposed upstream and downstream of an effluent discharge. The results highlighted a bioaccumulation of certain targeted emerging pollutants in three freshwater invertebrates, as well as inter-species differences. 18 out of 35 compounds were detected and eight were quantified. The highest concentrations were measured for ibuprofen in G. fossarum, reaching up to 105 ng g(-1).