AbstractPrior studies demonstrate that bottom velocity measurements from Doppler sonar systems are proportional to bedload transport rates. These observations suggest that acoustically based systems offer a capability for rapid sampling of bedload transport processes. Before these measurements can be fully utilized, validation and understanding of the sampling mechanism are essential. We explore the measurement mechanism through a series of laboratory trials with a field instrument, the multi‐frequency coherent Doppler profiler (MFDop). The MFDop system is a multi‐frequency (1.2–2.2 MHz), bistatic Doppler sonar that provides three‐component ensemble‐averaged velocity profiles over a ∼30 cm depth interval with up to 1 mm resolution at a rate of 50 profiles/sec. Tests of the MFDop system were carried out in the main flume in field‐scale conditions at the St. Anthony Falls Laboratory (SAFL) using 1 ms−1 mean flows over a mobile bed of sand with median grain size d50 = 0.4 mm. We find agreement between MFDop transport measurements and measurements based on bedform migration rates, and sediment traps built into the SAFL flume. Predictions using the Meyer‐Peter and Müller (1948) empirical equation closely match our observations while in contrast, predictions using the Nielsen (1992) equation are a factor of two higher.