Distinguishing between effects of natural and anthropogenic environmental factors on ecosystems is a fundamental problem in environmental science. In river systems the longitudinal gradient of environmental factors is one of the most relevant sources of dissimilarity between communities that could be confounded with anthropogenic disturbances. To test the hypothesis that in macroinvertebrate communities the distribution of species' sensitivity to organic toxicants is independent of natural longitudinal factors, but depends on contamination with organic toxicants, we analysed the relationship between community sensitivity SPEAR(organic) (average community sensitivity to organic toxicants) and natural and anthropogenic environmental factors in a large-scale river system, from alpine streams to a lowland river. The results show that SPEAR(organic) is largely independent of natural longitudinal factors, but strongly dependent on contamination with organic toxicants (petrochemicals and synthetic surfactants). Usage of SPEAR(organic) as a stressor-specific longitude-independent measure will facilitate detection of community disturbance by organic toxicants.