Oyster reefs play a crucial role in coastal protection by attenuating waves and currents, thereby contributing to coastal stability. This protective function is largely due to the significantly greater roughness height of oyster reefs than bare sand surfaces. There is limited understanding of the characteristic length and the appropriate estimation equation needed to determine the roughness height of oyster reefs. To address this, experiments were conducted under both unidirectional and oscillatory flow conditions to explore the relationship between the geometry of oyster reefs and their roughness height. The experimental results indicate a correlation between the hydraulic roughness height and the height of their surface rough elements. Furthermore, the study proposes a unified roughness height formula that is applicable to both unidirectional and oscillatory flows. The validity of this formula is assessed through its application to the log law and comparison with experimental data. The findings of this study facilitate the estimation of the roughness height of oyster reefs, which is essential for understanding their hydraulic characteristics and their role in coastal protection.