ABSTRACT Accurate assessment of bedload transport is a challenging task due to its variable nature in space and time. Bedload transport measurement techniques can be divided into two categories of direct and indirect methods. The focus of this study is on dune tracking as an indirect measurement method that has received much attention in recent years. However, a comprehensive workflow that allows the integration of this method into a routine measurement operation instead of or jointly with the direct sampling method has not been implemented yet. During a three-day measurement campaign conducted in the Rhine River, a detailed workflow for performing bedload transport measurements using the dune tracking method was introduced. Dune tracking validation was thoroughly evaluated, with significant efforts to simultaneously collect data using direct sampling. Direct measurements of bedload transport showed higher and more variable rates compared to dune tracking estimates. It was assumed that finer sediment fractions, moving as patches or small-scale superimposed bedforms were presumably not captured by the dune tracking. However, their significant contribution to bedload transport suggests that dune tracking estimates may have been underestimated. Further research is needed to explore how varying flow and sediment conditions affect bedload transport modes and measurement methods comparability.