Clogging characteristics of conventional sand filter layers with different grain-size distributions were experimentally studied to estimate their filtration capacity to capture non-point source pollutants in an artificial rainwater reservoir. A series of laboratory-scale chamber tests was conducted for artificial urban runoff synthesized with non-point source pollutants collected from a real road in Seoul, Korea. In addition, an analytical filtration model for estimating removal of non-point source pollutants was adopted considering the clogging characteristics. To evaluate the performance of three types of sand filter layers with different grain size characteristics, the pollutant concentration was measured in terms of total suspended solids and chemical oxygen demand. The lumped parameter (θ) related to the clogging property was estimated by comparing the accumulated weight of pollutant particles obtained from the laboratory chamber experiments and the theoretical estimation from the analytical filtration model. Based on the experimental study and theoretical consideration, a double-sand-filter layer consisting of two separate layers is proposed as the optimum system for removing non-point source pollutants in the pilot-scale rainwater reservoir.