Roof maintenance practices require biocides to fight against moss, lichens and algae growth. The main component of these products, in France, is benzalkonium chloride. This paper describes, on the base of bench tests, how benzalkonium spread on roofs contaminates the collected runoff during the following rain events. The results of the study show a huge contamination of roof runoff immediately after a treatment (from 5.5 to 27 mg/L) followed by a negative exponential decrease. The residual concentration in the runoff water remains greater than 0.1 mg/L even after more than 280 mm of rain depth. The benzalkonium leaching depends on the roofing material, as concentrations and total mass leached is fewer for clay tiles than for concrete tiles. Nevertheless the tests undertaken illustrate the fact that a large part of benzalkonium spread on tiles is lost. This may be explained by the degradation of the molecule.