Abstract  The aim of this study was to evaluate the cytotoxic and genotoxic potential of the wastewater (WW), the effectiveness of the treatment used by the wastewater treatment plant (WWTP) with sequential batch reactors (SBR) technology, and whether its final treated effluent (FTE) can compromise the water quality of the river at the location where it is discharged. We focused our research on six examples. For analytical chemistry and Allium metaphase (M) test all six samples were collected. Of these, three are so-called biotechnological patterns (WW, WW after mechanical step treatment and FTE), and three are natural riverine environmental patterns. For the micronucleus (MN) test, fish specimens were collected from three sites in the river Kamniška Bistrica. The first two sites locations are up and down the FTE outlet. Results from these areas were compared to the third site (not polluted) reference site, the so-called natural control group. Complementary study with analytical chemistry and biological tests shows that the treatment effect SBR in the Domžale–Kamnik central WWTP carried effectively proved to be efficient for the removal of the cytogenotoxic substances in treated effluent and  consequently in aquatic environment.