The hydraulic conductivity of riverbeds and shallow aquifers controls hyporheic flow and surface water-groundwater exchange, which is critical to aquatic systems. We show that the hydraulic conductivity of shallow alluvial aquifers subject to sinuosity-driven hyporheic flow is dynamic because of transport of fine materials. We analyze changes in hydraulic conductivity over one year at a meander-scale experimental river-aquifer system using water table monitoring, repeat in-situ hydraulic tests, grain size analysis, and flow modeling with particle tracking. Areas with relatively high initial hydraulic conductivity became more permeable after one year, while areas with lower initial hydraulic conductivity became less permeable. Particle tracking suggests fine materials were flushed from the more permeable portions of the aquifer and deposited in the less permeable areas down-gradient. Since hydraulic conductivity evolution has feedback on flow, static or synoptic hydraulic conductivity measurements in river-hyporheic-riparian systems may need to be revisited. Temporally changing hydraulic conductivity has the capacity to impact rates of ecological and biogeochemical processes.