SUMMARYLarge-eddy simulation (LES) of transitional separating-reattaching flow on a square surface mounted obstacle has been performed. The Reynolds number based on the uniform inlet velocity and the obstacle height is 4.5 × 10 3 . A dynamic subgrid-scale model is employed in this work. The mean LES results compare favourably with the available experimental and direct numerical simulation (DNS) data. Extensive analysis of the time series signals of the velocity and pressure fields at different locations including positions close to solid surfaces, at the centre and edge of the separated-reattached boundary layer using the windowed Fourier transform (WFT) and the wavelet transform was performed. The spectra analysis revealed the nature of the amplified frequencies at all the important locations of the flow field. Excited modes that could be due to the movement (shedding) of large-scale structures and pairing of such types of structures are identified. A clear frequency peak was captured just upstream of the separation line. The value of the frequency peak and the low percentage of the back flow velocity compared to the freestream velocity in the current case strongly support the idea that this amplified frequency is most likely due to the Kelvin-Helmholtz (K-H) instability mechanism of the shear layer forming in the boundary of the small upstream separated region rather than being attributed to the flapping of the shear layer.