Spatio-temporal characteristics of wall pressure fluctuations in separated and reattaching flows over a backward-facing step were investigated through an extensive pressure-velocity joint measurement with an array of microphones. The experiment was performed in a wind tunnel with a Reynolds number of 33 000 based on the step height and the free-stream velocity. Synchronized wavelet maps showed the evolutionary behaviour of pressure fluctuations and gave further insight into the modulated nature of large-scale vortical structures. To see the relationship between the flow field and the relevant spatial mode of the pressure field, a new kind of wavenumber filtering, termed ‘spatial box filtering’ (SBF), was introduced and examined. The vortical flow field was reconstructed using every single-point velocity measurement by means of the conditional average based on the SBF second mode of pressure fluctuations. The flow field showed a well-organized spanwise vortical structure convected with a speed of 0.6U0 and a characteristic ‘sawtooth’ pattern of the unsteady trace of reattachment length. In addition to the coherent vortical structures, the periodic enlargement/shrinkage process of the recirculation region owing to apping motion was analysed. The recirculation region was found to undergo an enlargement/shrinkage cycle in accordance with the lowpass-filtered component of pressure fluctuations. In addition, such modulatory behaviour of the vortical structure as the global oscillation phase was discussed in connection with the conditionally averaged flow field.