Bedload transport rate fluctuations have been observed over time in steep rivers and flumes with wide grain size distributions even under constant sediment feeding and water discharge. The observed bedload transport rate pulses are periodic and a consequence of grain sorting. Moreover, the presence of large, relatively immobile boulders, such as erratic stones, which are often present in mountain streams, has an impact on flow conditions. The detailed analysis of a 13 hours laboratory experiment is presented in this paper. Boulders were randomly placed in a flume with a steep slope (6.7%), and water and sediment were constantly supplied to the flume. Along with the sediment transport and bulk mean flow velocity, the boulder protrusion, boulder surface, and number of hydraulic jumps, which are indicators of the channel morphology, were measured regularly during the experiment. Periodic bedload transport rate pulses are clearly visible in the data collected during this longduration experiment, along with correlated fluctuations in the flow velocity and bed morphology. The links among the bulk velocity, the time evolution of the morphology variables, and the bedload transport rate are analyzed via correlational analysis, showing that the fluctuations are strongly related. A phase analysis of all observed variables is performed, and the average shapes of the time cycles of the fluctuations are shown. Observations indicate that the detected periodic fluctuations correspond to different bed states. Furthermore, the grain size distribution through the channel, which varies in time and space, clearly influences these bedload transport rate pulses. Finally, known bedload transport rate formulae are tested, showing that only the application of a drag shear stress allows a correct estimation of the time fluctuations.