The unsteady characteristics of flow separations induced by a forward-facing step immersed in thick oncoming turbulent boundary layers developed over smooth and fully rough upstream walls were experimentally studied using time-resolved particle image velocimetry. The upstream boundary layer thicknesses were 4.3 and 6.7 times the step height in the smooth and fully rough wall cases, respectively. The Reynolds number based on the step height and free-stream velocity was 7800. The effects of upstream wall roughness on the instantaneous separated shear layer, frequency spectra and two-point correlations are critically examined. Proper orthogonal decomposition (POD) is employed to investigate the mechanism underlying the unsteadiness of turbulent separation bubbles over the step. The first two POD modes exhibit the same topology in both cases. The energy fraction of the first mode is significantly larger in the rough wall case, signifying the enhanced large-scale motion residing in the incoming turbulent boundary layer. The correlation between the reverse flow area over the step and the first POD mode coefficient is much stronger in the rough wall case than in the smooth wall case. High levels of vertical fluctuating velocity immediately upstream of the leading edge of the step is mostly associated with the first POD mode in the rough wall case, but is further influenced by the higher POD modes in the smooth wall case. Irrespective of the upstream wall roughness, the vertical fluctuating velocity over the step are mostly induced by vortex shedding motion from the leading edge of the step.