Dissolved pollutant transport over the ground surface is one of the main contributors to water pollution in urban environment. However, existing widely applied transport models are semi-empirical and the mechanism of the dissolved pollutant runoff is still not well understood. A novel physically-based transport model for dissolved pollutant is herein proposed by adopting a “control layer” concept in the overland flow. This transport model assumes that the dissolved pollutant in the upper runoff water is completely mixed with that in the underneath control layer. To verify the proposed model, a series of laboratory experiments were conducted. It showed that the predictions made by the model are in good agreement with the experimental results. The depth of the control layer is mainly correlated with the bed slope and shows no obvious dependence on rainfall intensity. The minimum depth of the control layer is bounded by a limiting value. In addition, the maximum pollutant transport rate is found to occur at the time of concentration. The rainfall intensity, bed slope, surface roughness and catchment length are dominant factors that control the dissolved pollutant transport. The wash-off coefficient is a function of time and is found to be the reciprocal of the average water depth of the catchment area over which the equilibrium state has been reached. This study advances the understanding of the mechanism of the dissolved pollutant transport in urban environment.