Nonpoint source pollution (NSP) is one of the main factors leading to black odor in urban rivers. A better understanding and simulation of the formation and transport mechanism of NSP is critical to the development of effective urban rainwater management and pollution control strategies. This work presents a novel hydrodynamic-water quality coupling model to quantitatively simulate the entire physical process of the urban NSP by integrating two-dimensional (2D) NSP build-up, wash-off and transport modules into the source code of the GPU-accelerated surface water and transport (GAST) model. The advantages of this model are that high-resolution terrain is considered, such as key microtopography, such as roads and houses, which will have a diversion effect on the transport of hydrodynamic water quality and affect, and detailed hydrodynamic processes based on physical processes are fully considered. Additionally, a graphical processing unit (GPU)-based acceleration method is introduced to increase the parallel performance of the computing process. Three scales of cases were used to verify the model. First, indoor experimental data from the model roof and measured data from the campus roof under two short-duration rainstorms were used for nonpoint source model verification. The Nash-Sutcliffe efficiency (NSE), root mean square error (RMSE), Bayesian information criterion (BIC) and Akaike information criterion (AIC) were utilized to assess the applicability of the different NSP wash-off equations added to this model. Based on this model, the NSP mechanism processes of residential buildings were examined. The results indicate that this model is suitable for various pollutant wash-off formulas and is capable of high-efficiency and robust predictions of the sources, transmission paths, and spatiotemporal distribution characteristics of urban nonpoint sources. We quantitatively simulated the generation and transport of NSP from a single roof and proposed an NSP traceability method based on detailed hydrodynamic processes. This model can provide strong technical support for the precise treatment of urban NSP and the construction of sponge facilities.