Near the threshold of grain motion, sediment transport is “on-off” intermittent, characterized by large but rare bursts separated by long periods of low transport. Without models that can predict the presence of intermittency, measurements of average sediment flux can be in error by up to an order of magnitude. Despite its known presence and impact, it is not clear whether on-off intermittency arises from the grain activity (the number of moving grains) or grain velocities, which together determine the sediment flux. We use laboratory flume experiments to show that the on-off intermittency has its origins in the velocity distributions of grains that move by rolling along the bed, whereas grain activity is not on-off intermittent. Improved predictions of sediment flux require that the types of intermittency we identify be incorporated into stochastic models of sediment flux. Their recognition opens the door to physically based uncertainty estimates of time-averaged sediment flux.