The effect of environment contaminants on genome instability and changes in enzyme activity (acetylcholinesterase (AChE), glutathione S-transferase activities (GST), etoxyresorufin O-deethylase (EROD) and metallothionein (MT)) of Chironomus riparius Mg. from Bulgarian and Turkish stations over two years (2009, 2010) as well as laboratory reared larvae were studied. Physicochemical analysis of the sediments from the field stations indicated the presence of heavy metal pollutants (Cr, Cu, Mn, Pb, and Cd) whose concentrations were higher than the reference data. Genome instability was determined by somatic structural and functional alterations of the polytene chromosomes. In the field sites of both countries somatic aberrations occurred at a significantly higher frequency (p < 0.001) compared with control and laboratory material. C. riparius in sediments with higher concentrations of trace metals (Derincay River, Turkey and Chaya River, Bulgaria), was found to possess a high spectrum of somatic chromosome rearrangements with a somatic index of 2.53 and 3.25 respectively. Changes in functional activity included decreased activity of the Balbiani rings (BRs) and nucleolar organizer (NOR). The observed chromosome alterations agree with the high degree of trace metal pollution and high activity of the studied enzymes. However, no correlation between single somatic chromosome rearrangements and concentrations of specific metal ions was defined. The data are discussed in the light of the wide variety of interactions of metals in nature. The results show that the genome response and biochemical markers are sensitive markers of toxicity and provide early warning indicators of contaminants in the environment.