The benthic compartment of River-dominated Ocean Margins (RiOMar) is largely affected by sedimentary processes, as well as by natural and anthropogenic disturbances. Recent studies have confirmed the major importance of riverine inputs and local hydrodynamics in the spatial structuration of low- and high-energy temperate RiOMar, respectively. Differences in the nature of these structuring factors could also affect the temporal dynamics of these two types of systems. The present study is aiming at: (1) quantifying spatiotemporal changes in surface sediment and benthic macrofauna within the West Gironde Mud Patch (WGMP; high-energy system) over both short (2016–2018) and longer (2010/2016–2018) time scales, (2) identifying the main environmental factors explaining those changes, and (3) achieving a comparison with the Rhône River Prodelta (RRP; low-energy system) in view of further characterizing the functioning of the benthic components of these two temperate RiOMar. Surface sediment characteristics (grain size, quantitative and qualitative descriptors of particulate organic matter) and benthic macrofauna compositions were assessed based on 4 seasonal sampling of 5 stations located along a depth gradient within the WGMP. Results highlighted the existence of spatial patterns for both surface sediment and benthic macrofauna, which are both better explained by local hydrodynamics. Most variables presented seasonal changes. Benthic macrofauna compositions also showed pluri-annual changes, which were attributed to a cicatrization process following a major disturbance caused by the 2013–2014 series of severe winter storms, and suggests the major role of local hydrodynamics in explaining 2010/2016–2018 temporal changes in WGMP benthic macrofauna compositions. The comparison with the RRP further highlighted major discrepancies between the two systems in the main processes (i.e., hydrodynamics versus river hydrological regime) explaining surface sediment characteristics and benthic macrofauna compositions, which supports current RiOMar typologies.