Nitrogen (N) and phosphorus (P) were measured in atmospheric deposition and roof runoff in Beijing, China from May to October 2009. Serious N pollution caused by summer rainfall was found in Beijing. N was mainly transported in dissolved from, while P was predominantly found in its particle form. Bulk deposition potentially accounted for as much as 70%, 71%, 97%, and 45% of total nitrogen (TN), dissolved nitrogen (DN), total phosphorus (TP), and dissolved phosphorous (DP) loads in roof runoff, respectively, indicating that atmospheric deposition predominantly contributes to roof runoff pollution in Beijing. Moreover, wet deposition was an important source of TN, DN, and DP, while dry deposition was the main source of TP. N and P concentrations in roof runoff decreased as the amount of rainfall increased. The monthly loads of N and P in roof runoff were linearly and positively correlated with the amount of rainfall, indicating that the amount of rain is an important factor that influences the N and P loads in roof runoff. The positive relationship between N and P fluxes (load divided by the dry weather period; mg/m²d) and the mean daily rainfall intensity (amount of rainfall divided by the dry weather period; mm/d) suggest that N and P loads in roof runoff can be estimated by measuring the amount of rainfall and the antecedent dry weather period.