This paper proposed a Monte Carlo based method to quantify non storm water flow entries into storm drains, in conjunction with mass balance of marker profiles between sources and exit. The proposed model was applied to a separate storm and sewer system in Shanghai, China. The sanitary sewage, semiconductor wastewater and groundwater with inappropriate entries into storm drains were quantified using acesulfame and total nitrogen, fluoride, total hardness as marker species respectively. Compared with the traditional deterministic approach, the proposed approach is able to account for the measurement errors and the impact of variability of the source marker profiles resulting from the spatial heterogeneities and therefore presents reliable source flow components that add up to 100%. Good precision was found between simulated and measured data, with a relative error of less than 10% in this case. The guideline to establish data library of marker species was also presented.