Heavy metal concentrations were surveyed in several species of aquatic macrophytes and in sediments of a lake and four rivers from Macedonia, northern Greece. Acid digestion of sediments and plant material and the subsequent use of atomic absorption spectrometry were the analytical methodologies followed for the analysis. Values were variable within each species while differences in metal contamination among the studied water ecosystem were also found. The lake was less contaminated than the rivers, the contamination of which is dependent on the metal species. Sediment had greater Cu, Pb, and Ni contamination than the aquatic plants, whereas the reverse was the case for Zn, Cd, and Mn. The mean heavy metal contents of the sediments and aquatic plants were in the descending order of Mn > Zn > Ni > Cu > Pb > Cd, whereas in the accumulation of metals by plant tissues, the corresponding order was root > rhizomes > leaf > flower > stem > seed.