The global framework of this study is to go further in the understanding of the involved mechanisms of uranium and selenium internalisation at the subcellular level and of their toxicity towards several aquatic organisms. In this context, the applications and performances of a Scanning Transmission Electronic Microscope (STEM), which is fitted with a CCD camera and an Energy-Dispersive-X-Ray (EDX) analysis are reported. This equipment provides a direct correlation between a histological image (0.34 nm resolution) and a clear expression of element distribution. Demonstration of the usefulness of this method to understand the bioaccumulation mechanisms and to study the effect of the pollutant uptake at the subcellular level has been performed for target organs of a metal (U) and a metalloid (Se) in various biological models: a freshwater crayfish (Orconectes Limosus) and a unicellular green alga (Chlamydomonas reinhardtii)). TEM-EDX analysis revealed the presence of U-deposits in gills and digestive gland in crayfish. In the alga, the accumulation of Se was found in electron-dense granules within the chloroplast with ultrastructural changes and starch accumulation.