This paper reports on studies of the effect of heavy metals on the Chironomidae that inhabit the Matylda stream, which has been contaminated for about 100 years by discharge water from a zinc and lead ore mine. Stream sediment was strongly polluted by Cd, Pb, Cu and Zn. These metals did not affect the Chironomidae community but strongly changed the genome system of the Chironomidae species that inhabited the sediment. The salivary gland chromosomes of six species belonging to the two genera Chironomus and Prodiamesa are analyzed. In all species the somatic index is calculated on the basis of somatic * Corresponding author: szarek@iop.krakow.pl chromosome alterations. Chironomus riparius has the highest numbers of somatic alterations and the highest somatic index -9.67. The smallest chromosome G carries the key structures known as "Balbiani rings", which play an important role in species development. This chromosome is very sensitive in the genome of the most studied species. The high sensitivity of the C. riparius genome is discussed in light of its DNA organization. The results show a high response of the salivary gland chromosomes to heavy metal pollution, and this makes them a valuable indicator in the assessment of water quality and detection of mutagenic agents in the aquatic environment.