Hyporheic flow in streams has typically been studied separately from geomorphic processes. We investigated interactions between bed mobility and dynamic hyporheic storage of solutes and fine particles in a sand-bed stream before, during, and after a flood. A conservatively transported solute tracer (bromide) and a fine particles tracer (5 μm latex particles), a surrogate for fine particulate organic matter, were co-injected during base flow. The tracers were differentially stored, with fine particles penetrating more shallowly in hyporheic flow and retained more efficiently due to the high rate of particle filtration in bed sediment compared to solute. Tracer injections lasted 3.5 h after which we released a small flood from an upstream dam one hour later. Due to shallower storage in the bed, fine particles were rapidly entrained during the rising limb of the flood hydrograph. Rather than being flushed by the flood, we observed that solutes were stored longer due to expansion of hyporheic flow paths beneath the temporarily enlarged bedforms. Three important timescales determined the fate of solutes and fine particles: (1) flood duration, (2) relaxation time of flood-enlarged bedforms back to base flow dimensions, and (3) resulting adjustments and lag times of hyporheic flow. Recurrent transitions between these timescales explain why we observed a peak accumulation of natural particulate organic matter between 2 and 4 cm deep in the bed, i.e., below the scour layer of mobile bedforms but above the maximum depth of particle filtration in hyporheic flow paths. Thus, physical interactions between bed mobility and hyporheic transport influence how organic matter is stored in the bed and how long it is retained, which affects decomposition rate and metabolism of this southeastern Coastal Plain stream. In summary we found that dynamic interactions between hyporheic flow, bed mobility, and flow variation had strong but differential influences on base flow retention and flood mobilization of solutes and fine particulates. These hydrogeomorphic relationships have implications for microbial respiration of organic matter, carbon and nutrient cycling, and fate of contaminants in streams.