The area of the Dunajec river basin includes several geological units in the Central Carpathian region at the Polish-Slovakian borderland. The paper focuses on the geomorphometric parameters of the drainage system to recognize the influence of the deep seated geological structures on the morphology of the Dunajec river basin (Central Carpathians). The study were enriched with analysis of the geological maps and lineaments extracted from Digital Elevation Model. According to the obtained results, the massive NW-SE trending fault zones play a vital role in the geological architecture of the researched area. The development of the secondary fault structures has been determined by these dislocations and the manifestation of their activity can be observed as deformations of some of the other tectonic structures along the main fault zones, especially at the folds’ axes. Additionally, the geometric and morphometric features of the drainage system have also been influenced by the activity of these deep structures. The tectonic activity represented by the level of morphological rejuvenation, visible in the light of the morphometric parameters of the streams and the drainage basins, varies greatly between the tectonic units. This diversity is caused by both the lithological and structural features of these geological units.