Dunes form annually on the sand bed of the tidally influenced South Arm of Fraser River, British Columbia. Bathymetric surveys along the center of the main channel throughout a snow-melt freshet provided measurements of dune geometry and migration. Dune length, height, and steepness all increase with river discharge. However, lag between the highest flow conditions and development of the largest, steepest dunes reflects the influence of antecedent flow conditions on dune geometry. Population averages of dune height and steepness ratio change more rapidly than dune length, whilst coefficients of variation of dune height, length, and steepness ratio indicate high variability in dune geometry within the estuarine reach during periods of dune growth and decay. Unlike dune geometry, dune migration rates display little lag with flow conditions. The largest coefficients of variation for dune migration occur during periods of rapid change in discharge and tidal fall, corresponding to the onset of rapid change in dune geometry on both rising and falling limbs. Migration rate estimates and geometry measurements are used to estimate associated sand transport. In the absence of hydraulic measurements in the estuary, Mission and Hope discharges are adopted to drive simple statistical models of sand transport as a function of discharge and tidal fall. The models cover 65–70% of the transport, and tidal fall is only marginally significant. Comparison with historical direct measurements indicates that the dune-associated transport coincides with bed-load transport in the estuary, and arguments are made that it constitutes the preponderance of all bed-material transport.