Apart from being a protection layer against subgrade attrition, the subballast of ballasted rail tracks is designed mainly to act as a stress dissipation layer or more commonly known as a capping layer. When considered as a filtration layer, subballast would prove to be inadequate due to the use of design criteria that are primarily based on steady seepage loading common in embankment dams. The seepage hydraulics through porous media would have to be influenced by the cyclic mechanical loading generated by the passing trains. Under the influence of cyclic train loading, subballast particles rearrange and attempt to attain a more stable configuration through the process of vertical settlement, lateral spreading, and particle degradation. The deformability of the pore medium itself would then affect the filter condition due to the changes in porosity and its subsequent impact on permeability. This paper presents a new design method that considers the effectiveness of the subballast as granular filter being dependent on the reduction of its porosity and permeability over time. The main factors that are found to contribute to the reduction in porosity within the subballast layer are (a) the plastic deformation generated by the cyclic load from the passing traffic, and (b) the accumulation of migrating fines trapped within the filter voids. Laboratory test results conducted on a novel cyclic loading permeameter apparatus were used to validate the proposed method. Two worked out examples are provided.