The Ojców National Park is situated in southern Poland in an area of Jurassic limestone, which determines the hydrochemistry of the water in the River Prądnik. The geochemical index of the sediment in the River Prądnik indicated it is moderately polluted with Pb and Zn, and heavily polluted with Cd compared to unpolluted sediment. The effect of natural and anthropogenic sources on the sediment in the River Prądnik and in appearing of structural and functional alterations in the salivary gland chromosomes of two species of Chironomidae, Micropsectra pallidula and Polypedilum convictum, was investigated. Two types of chromosomal rearrangements (inherited and somatic) were identified in the species studied. Inherited heterozygous inversions occurred at a higher frequency (between 5.55%–57.81%) and may have local adaptive value. In M. pallidula a karyotype divergence consisting of fixed chromosome inversions on arms B and E was recorded. As somatic chromosome rearrangements can be caused by stress agents, we suggest that the somatic aberrations in both of the species studied indicate the existence of pollution, i.e. induced stress. On the basis of these somatic rearrangements the somatic index of both species was defined: M. pallidula – 0.346, P. convictum – 0.555. In addition to these rearrangements functional alterations in key structures, Balbiani rings (BRs) and the nucleolar organizer region (NOR) located on chromosome EF, which significantly decreased their transcriptional activity, were recorded in M. pallidula. Changes in the appearance of the telomere region on chromosome G in P. convictum was considered to be a response to the environmental conditions in the River Prądnik. It was shown that polytene chromosomes are very sensitive to environmental changes and can be used to detect pollutants in aquatic ecosystems., Paraskeva Michailova ... [et al.]., and Obsahuje seznam literatury