In first part of the paper a review is given on fractionation methodologies by sequential extraction methodologies applied for risk assessment of environmental pollution by potentially toxic elements (PTE). Main sources of PTE release are the mining-, industrial-, agri-food production-, traffic- and communal-waste. In this latter the medical and health care sources may emerge due to therapeutic and diagnostic applications (Ag, As, Au, Ba, Bi, Cd, Ga, Gd, 131I, Ir, Li, Mn, Fe, Os, Pd, Pt, Rh, Ru, Sb, Sn, Ti, V), to nanomedicines, to ayurvedic herbal medicines with possible contaminant PTEs and non-controlled dietary supplements. The magnitude of adverse effects caused by PTEs in the soil-water-sediment system depends on the various chemical species that can arise. Long-term biological impacts are strongly influenced by mobilization-immobilization processes in the aquatic environment. These can be studied through sequential extraction procedures modelling their pathways. In Europe the simplified extraction scheme proposed by BCR in 1993 and modified in 2001 is mostly used for this purpose. By this approach samples are gradually decomposed and four different fractions of PTEs can be identified, i.e.: i) water-soluble and carbonate-bound fraction; ii) fraction associated with reducible Fe- and Mn-oxides; iii) organic complexed fraction and sulphides; iv) fraction soluble in oxidative acids. The sediment-based Certified Reference Material (CRM) BCR 701 was produced to check the accuracy of the fractionation procedure. The standardization process was hindered by methodological problems, i.e.: i) the solvents used in the BCR system do not mirror completely the natural mobilization processes and partly modify the original chemical species; ii) the time demand of the batch leaching extraction steps is exceedingly long (4–5days); iii) the above CRM, certified for the fractionation of Cu, Cd, Cr, Ni, Pb and Zn, is available only for sediment and cannot be applied to other environmental matrices and other PTEs. The studies aimed at improving the BCR methodology are summarized, in particular to: i) develop continuous flow systems; ii) accelerate the BCR leaching steps by sonication; iii) extend the BCR procedure to other environmental matrices (soils, red mud, composts, biofilms) and further PTEs by multielemental (ICP-OES) detection.In second part of the paper a case study is presented for evaluation of long-term changes of the environmental mobility of PTE contaminations in the fish pond system of Gödöllő town. For vertical and horizontal mapping of PTE content of accumulated sediment layers core samples were taken in 1994, 1995 and 2013. In the sediment layers total soluble PTE content was related to the BCR fractionation. The Chernobyl origine radionuclides were detected by γ-spectroscopy. The BCR sequential extraction procedure for tracking the long-term fate of PTE contamination of different origine in surface water/sediment/systems showed a much potential. By repetition of fractionation of PTEs after 20years clearly reflects the change of PTE concentrations in different fractions. The decrease of PTE concentrations can be explained by leaching the most mobile fractions by water exchange over the sediment and/or by remediation activity.