Understanding bed load transport fluctuations in rivers is crucial for development of a transport theory and for choosing a sampling interval for “mean” transport rates. Field-scale studies lack sufficient resolution to statistically characterize these fluctuations, while laboratory experiments are limited in scale and hence cannot be directly compared to field cases. Here we use a natural-scale laboratory channel to examine bed load transport fluctuations in a heterogeneous gravel substrate under normal flow conditions. The novelty of our approach is the application of a geometrical/statistical formalism (called the multifractal formalism), which allows characterization of the “roughness” of the series (depicting the average strength of local abrupt fluctuations in the signal) and the “intermittency” (depicting the temporal heterogeneity of fluctuations of different strength). We document a rougher and more intermittent behavior in bed load sediment transport series at low-discharge conditions, transitioning to a smoother and less intermittent behavior at high-discharge conditions. We derive an expression for the dependence of the probability distribution of bed load sediment transport rates on sampling interval. Our findings are consistent with field observations demonstrating that mean bed load sediment transport rate decreases with sampling time at low-transport conditions and increases with sampling time at high-transport conditions. Simultaneous measurement of bed elevation suggests that the statistics of sediment transport fluctuations are related to the statistics of bed topography.