The distribution of heavy metals in two lakes of high ecological significance, Doirani and Kerkini, located in Northern Greece was studied. Eight metals (Cd, Cr, Cu, Fe, Mn, Ni, Pb and Zn) were determined in water, total suspended solids, fine and coarse sediments. Moreover, the modified BCR fractionation scheme was employed in sediments and suspended solids to determine soluble, oxidisable, reducible and residual fractions of metals. The Lake Doirani presents higher metal concentrations in aqueous phase than Lake Kerkini; Cd, Cu, Ni, Pb and Zn are above the chronic freshwater quality criteria for aquatic life. In both lakes, Fe and Mn are the most abundant elements in total suspended solids whereas Cd the less abundant. The Lake Kerkini exhibits higher concentrations of all the examined metals in sediments comparing to the Lake Doirani, however the concentrations are lower than the sediment quality guidelines. Cd in sediments is mainly in soluble fraction, Pb and Cu exhibit significant oxidisable fractions whereas, Cr and Fe associated mainly with residual fraction. (C) 2007 Elsevier B.V. All rights reserved.