Multi-scale factors controlling fine sediment interstitial storage along a river continuum with contrasted bedload transport conditions

Human alterations have disrupted sediment dynamics in European rivers, leading to sediment starvation, channel incision, and excessive deposition of fine sediments within gravel bed interstices. This interstitial infilling, when intensified by anthropogenic pressures, promotes hyporheic clogging and degrades habitat quality. Yet, the spatial and temporal dynamics of fine sediment storage in dam-associated bypassed reaches remain poorly documented, particularly where sediment replenishment is implemented. To fill this knowledge gap, we conducted a three-year multi-site study along 329 km of the Rhône River (France), encompassing armoured, gravel-replenished, and dynamic reference reaches. Sampling stations were restricted to riffles in order to minimize hydraulic variability linked to differences among geomorphic units. Interstitial fine sediment content was quantified using a cylinder core sampler. Results indicate that the variability in interstitial fine sediments is mainly driven by station-scale factors related to hydraulic conditions (i.e., grain size distribution of the bed and flow velocity). By minimizing station-scale effects using a quantile regression model, inter-station variability exceeds intra-station variability (over time), highlighting the strong influence of reach type. Armoured reaches, characterised by a coarse-grained fixed bed, has higher fine sediment contents than replenished reaches and reference reaches, the latter exhibiting the lowest fine sediment content. At two armoured stations, fine sediment contents exceed 25%, suggesting potential ecological impairment of the hyporheic zone. Temporal variability was limited, even after periods of high-flow conditions. These findings emphasize the need for multi-scale monitoring to disentangle station, reach and catchment-scale drivers, and for complementary methods to assess clogging potential more directly. • Interstitial fine sediment storage in riffles quantified using a cylinder core sampler • Interstitial fine sediment dynamics assessed in dam-associated bypassed reaches • Station-scale hydraulic conditions dominate interstitial fine sediment variability • Armoured reaches store more fines than gravel-replenished or reference reaches • Inter-station variability exceeds temporal variability despite high-flow events