Research in the 1990s showed that bed‐material transport rates could be estimated at the reach scale in both one‐dimension and, over small spatial scales (10s of m), in two‐dimensions. The limit on the latter was the spatial scale over which it was possible to obtain distributed data on morphological change. Here, we revisit the morphological method given progress in both topographical data acquisition and hydraulic modelling. The bed‐material transport needed to conserve mass is calculated in both one and two dimensions for a 1600 m × 300 m Alpine braided river “laboratory”. High‐resolution topographical data were acquired by laser scanning to quantify Digital Elevation Models (DEMs), and morphological changes caused by the flushing of the water intake were derived from repeated surveys. Based on DEMs of differences, 1D bed‐material transport rates were calculated using the morphological method. Then, a 2D hydraulic model was combined with a topographic correction to route sediment through the network of braided channels and to obtain a spatially variable estimate of transport in both downstream and cross‐stream directions. Monte Carlo simulation was applied to the routing model parameters, allowing identification of the most probable parameter values needed to minimize negative transport. The results show that within‐section spatial compensation of erosion and deposition using the 1D treatment leads to substantial local errors in transport rate estimates, to a degree related to braiding intensity. Even though the 2D application showed that a large proportion of the total transport was actually concentrated into one main channel during the studied low flow event, the proportion of transport in secondary anabranches is substantial when the river starts braiding. Investigations of the effects of DEM resolution, competent flow duration and survey frequency related to ‘travelling bedload’ and sequential erosion‐deposition emphasized the critical importance of careful data collection in the application of the morphological method.