Results are presented for a novel experimental investigation of live-bed scour at a cylindrical pier in covered flow. The experimental campaign also comprehended a reference scour test in clear-water conditions. Results showed that the time to achieve a dynamic equilibrium was a decreasing function of the flow rate. The same was found for the mean depth around which the scour fluctuated after equilibrium. The bed elevation was simultaneously measured within the scour hole and upstream of it to investigate the bed-form control of the scour fluctuations. Taking advantage of a high temporal detail used for the measurements, several statistical tools (cumulative frequency distributions, autocorrelation functions and spectra) were employed to characterize the properties of bed form and scour fluctuations. Amplitudes of the scour fluctuations were similar to those of incoming bed forms. On the contrary, a difference in the temporal scales for bed forms and scour fluctuations was detected and explained recognizing a mechanism of bed-form coalescence in the scour hole. The presented results enabled a phenomenological depiction of the process to be obtained, and are significant for analysis of scour data and also for engineering purposes.