Clogging of the filter media which is brought by physical, chemical, and biological factors tend to reduce the lifespan of filters and remains a challenge. In this study, a laboratory column test method was used to investigate the evolution of physical and biological clogging in a non-vegetated filter media system with layers of sand, gravel, and woodchip. Blank column tests using either sand or gravel were conducted and investigated. Several column setups with varying arrangements and particle sizes of sand and gravel were also prepared to identify the best filter media combination that is least susceptible to clogging without compromising the treatment capacity. Artificial stormwater runoff was introduced in the system at a specific hydraulic loading rate (HLR) and influent characteristics. The degree of clogging was quantified by monitoring the variations in the hydraulic head at different levels of the columns. Water samples were also collected, tested, and analyzed at the end of each test run in order to measure the treatment efficiency of the filter. The insights and results of this study can justify the physical and biological clogging formation in filter media and therefore be used to suggest some filter media particle size modifications that can help to improve the sediment removal and treatment performance. Moreover, it can also aid to reduce the maintenance frequency and costs of a stormwater filter system.