Time varying mass engineering structure is the type of structure where the total mass of the structure changes rapidly, and the loads generated are dependent on the properties of the structure, discharge rate and the properties of the materials inside the structure. A discharging silo is a typical time varying mass civil engineering structure where the total mass of the entire structure changes during the discharge of the stored materials. This paper presents a novel combinatory approach using Hilbert Transform and Variational Mode Decomposition methods to analyse nonlinear and non-stationary signals collected from the experimental silo filled with iron ore and one filled with sand. In particular, the silo filled with sand was producing loud foghorn like sound during discharge. The results revealed the existence of a frequency spectrum that can be developed further to assess the structural integrity of a time varying mass civil engineering structure such as a silo without the impacting silo operation and throughput. The obtained frequency spectrum shows that there is a noticeable difference between the spectra for the silo filled with iron ore and the silo filled with sand.