In the oligotrophic context of the Mediterranean Sea, riverine inputs of particulate organic matter represent an important source of food for benthic communities. However, since most of these inputs are delivered during short, but intense flood events, communities living in the vicinity of river mouths are also exposed to strong and frequent physical disturbances. A very tight and complex relationship links river dynamic and macrofaunal communities in Mediterranean deltas, but less is known on the response of meiobenthic communities to river regime. In 2010, sediments cores were collected in the Rhône River prodelta in winter and spring before the flooding of the Rhône River tributaries in June, and then twice in the early and late summer. The hypothesis was that increased runoff and export of terrigenous material would induce major changes in the sediment biochemistry, which would in turn trigger modifications in abundances and vertical distribution of the meiofauna. The origin and quality (lability, degradation state) of the different pools of organic matter preserved in these recent sediments were determined using bulk geochemical and molecular analyses (fatty acids, amino acids). Vertical profiles of descriptors for organic matter origin and quality revealed major changes in the nature of the inputs occurring at monthly time scales. Inputs of plant detritus from autumnal and winter flood events were still visible in the cores collected in February and April. A few days after the June 2010 high-discharge event, a newly deposit (∼7 cm) containing soil organic matter has recovered the prodeltaic sediments and the resident meiofaunal community, but at the end of August only 2 cm of this deposit remained. Multivariate analyses furthermore highlighted that the meiofaunal community was driven by both the trophic conditions and deposition of a new sediment layer driven by the hydrological regime of the Rhône River. In April, increased abundances of meiofauna were observed in response to the sedimentation of labile organic matter after the spring bloom. The June high-discharge event affected the meiofauna with a reduction of its abundance and the burial of the resident meiobenthic community. However, the meiofauna recovered in less than two months after this disturbance, showing the strong resilience of this component of the benthic ecosystem in this high energy environment.