The influence of boulders in high gradient gravel‐bed rivers can be significant. Yet few studies have isolated their role in regulating bedload. It is hypothesized that boulder relative submergence and the corresponding eddies developing around boulders affect the frequency of bedload pulsations and the location of sediment deposits. Results show the occurrence of two distinct timescales in bedload exiting a boulder array, which were identified via time series analysis. These are the small‐scale periodicity, PS, and the large‐scale periodicity, PL. PS was identified in the range of 4–6 min and is believed to result from congested bedload movement due to reduced conveyance area within the array. PL was identified in the range of 8–46 min. It is suggested that PL corresponds to large bedload releases around boulders, which the authors consider to be caused by feedbacks between boulder eddies and bedload deposits. It is also found that boulder submergence and Froude number, Fr, influence the location of predominant deposition. At High Relative Submergence, deposition occurs in the boulder wake regions. At Low Relative Submergence, deposition instead occurs upstream of boulders in locations that depend on Fr. For Fr < 1, material deposits in the stoss of boulders due to the necklace structure of the horseshoe vortex. However, for Fr > 1, material deposits at the flanks of boulders due to the influence of local wave crests around boulders. The trapping efficiency of boulders reduces the dimensionless mean bedload transport rate by three orders of magnitude compared to conditions without boulders.