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Harbour structures experience arbitrary loading conditions due to various hydrodynamic forces, wave forces during its design life along with subsoil-loss at support due to scouring, leading to considerable change in its free length. Since cumulative effects of these forces affect the strength and stability of the super-structure, techniques are required to monitor the free length of these piles, in particular due to sub-soil loss. The available technology for monitoring of such phenomenon is based on under-water instrumentation, but they are not cost effective and also need to be re-installed after a period. That's why vibration based techniques are attracting the eyeballs of many researchers. The application of these vibration based methods to detect and control the effect of scour has become advanced topic of research in recent years. In this study the effect of change in free length (due to subsoil-loss) on the natural frequency of a pile foundation system has been studied using a laboratory scaled model. The results were validated using SAP2000 and Abaqus CAE. This short investigation proposes a method to find out depth of sub-soil loss for an observed natural frequency.