Channel-bed armor can help to limit bedload-transport rates in coarse-bedded channels. In these systems, periodic large bed elements often exist with small deposits of fine material in the wakes of these boulders. A combined field and flume study was conducted to investigate the potential impact of these wake deposits on bedload-transport rates. Detailed sediment characterizations were performed on subsurface, surface and wake sediments in two coarse-bedded Connecticut rivers. Bedload measurements also were conducted at moderate and low flow in these two systems to determine the size distribution of bedload material. A 6-m long, 0.5-m wide flume was used to model these systems with fine sediment passing over a fixed-bed of sediment particles with uniform-sized, large bed elements. Sediment distributions of the wake deposits in the two Connecticut channels indicate the wake deposits may be produced from winnowing of sediments from the surface layer. Wake deposits also have sediment distributions similar to bedload-sediment distributions at low and moderate flow. Flume experiments show an increase in bedload-transport rate following changes in discharge versus steady-flow conditions. Even with decreases in discharge, bedload-transport rates show an increase versus the steady-flow state. The results demonstrate that sediment wakes establish a temporary dynamic equilibrium for a given discharge. Either increases or decreases in discharge disrupt this equilibrium condition and increase sediment delivery to the main flow. The study suggests that the influence of the rate of change in discharge may be as important as the absolute magnitude of discharge on sediment-transport rates at moderate and low discharges in sediment-limited systems.