The content of biogenic substances, i.e. ammonia (NH4+), nitrates (NO3–) and phosphates (PO43–), in the mountain stream waters was studied. The test (zero) sample was the water flowing from forest areas, while the study samples included the water from the streams flowing through extensively used sheep pastures. The impact of grazing on the water quality during high (in the rainy season) and low (in the dry period) water flows was assessed. The studies demonstrated the water contamination with ammonia, particularly during the rainy season. The contamination was also present in the test sample, so it cannot be attributed to the grazing activity. The highest nitrate concentrations were reported in the dry period. An influence of grazing on the migration of nitrates into waters was found, however, on a scale causing no contamination. The water contamination with phosphates was found. The studies demonstrated that extensive grazing did not affect the fertilisation of mountain stream water, yet the water quality may be deteriorated by the surface runoff processes and soil cover erosion.