AbstractUnderstanding the effects of human disturbance on the bedload transport regime of anthropised rivers is a topic of growing importance, as such information is of interest for adequate river diagnosis, correct implementation of restoration measures and appropriate design of post‐action monitoring programs. However, such assessments are complex, especially in sites where multiple factors simultaneously influence the bedload transport regime, so that it is difficult to establish simple causal relationships between human disturbances and changes in the sediment transport regime, notably on bedload. To overcome this, there is a need for rigorous hypothesis‐driven approaches to assess the isolated effects of each driver. With this in mind, we have characterised the dynamics of bedload transport in the Upper Garonne (Central Pyrenees, Spain‐France), a river impacted by sediment retention, flow diversion and mining that influence its morphological conditions and transport regime. We assessed the effects of (1) surface grain size distribution, (2) river morphology, (3) sediment supply and (4) flow diversion on the bedload transport regime. Four sites with different degrees of river anthropisation were selected. After defining hypotheses on the most likely bedload transport conditions for each site, we proposed a set of discriminating criteria to test these hypotheses, based on temporal within‐site and spatial between‐site comparisons of coarse particle tracking measurements over four years. The results of this research showed that the hydrosedimentary regime of the Garonne is controlled by a complex combination of drivers such as valley physiography, which exerts a first‐order control on differences in reach‐scale bedforms and bedload dynamics; and human disturbances which contribute to a reduction in sediment supply through changes in land cover and hydropower dams, or to changes in hydrology (i.e., flow competence) due to water diversion and abstraction.