Alpine headwater streams are characterized by extremely low nutrient concentrations and highly diverse flow regimes. Despite their remoteness, they can be subjected to inputs of wastewater from mountain huts or small wastewater treatment plants. The quality of this wastewater as well as the potential effect on the receiving alpine streams´ structure and function is poorly understood. Here we analyzed the wastewater effluent from Eleven huts situated close to headwater streams in two Spanish National Parks. Nine were equipped with septic tanks and three included a secondary treatment (ST). The effluents of the septic tanks provided on average up to 30 times more ammonia than the effluents of the STs. In six cases the effluent acted as a point source of nutrients, modifying stream water chemistry and, in particular, increasing ammonia concentrations at downstream sites. Despite resulting low nutrient concentrations (avg. 0.02 ppm N-NH4) at downstream sites, longitudinal uptake rates calculated for ammonia, nitrate and nitrite, indicate a stimulation of nitrification activity. Moreover, preliminary results from 16S rRNA gene sequencing indicate that the microbial community downstream the effluent shifts towards an increase in nitrification-related organisms. These results show effluent imprints on the structure and function of the receiving alpine streams despite naturally high dilution capacities and low N concentrations.