As a successive alkalinity-producing system pond for purifying mine drainage is operated, sediment accumulates in the limestone layer of the pond, and as the amount of accumulated sediment increases, the water permeability and treatment efficiency of the pond decrease. Hence, a flushing system is required, comprising of a network of perforated pipes installed in the limestone layers, to periodically discharge sediment and mine drainage to the outside. The performance of a flushing system depends on four distinct characteristics of the system: the characteristics of the limestone layer, the sediment, the flow, and the flushing device. However, existing studies have evaluated the performance of the entire system without considering these conditions. In this study, a new experimental method for designing a flushing system is proposed. This method is based on an experiment to evaluate the influence radius of orifice, which is the radius of the spherical volume around an orifice that can suck sludge by flushing. The results showed that the flow rate of water through the orifice in the glass bead layer matched well with the Blake–Kozeny formula, and that the greater the diameter of the orifice, the greater the influence radius of orifice. The influence radius of orifice according to the diameter and spacing of the orifice was evaluated, which provides a key criterion for designing a flushing system.