Spatial and temporal variations in groundwater As concentrations are mainly caused by changes in geochemical and hydrodynamic conditions. In this study, the effects of geochemical and hydrodynamic transiency on As desorption and transport in a layered heterogeneous system with preferential flow paths during continuous or intermittent water extraction were investigated. A flume desorption experiment was performed after an adsorption experiment lasting 99 d with competitive adsorption anions (phosphate) in the influent. The results indicated that although competitive adsorption between As and phosphate at the water/solid interface significantly promoted As desorption from solid materials, marked amounts of As desorbed slowly or were on irreversible sorption sites in the system. As adsorbed by the sand and clay near the preferential flow paths was preferentially released, while the release of As from the interiors of the clay zones was limited by diffusion. Water extraction accelerated As transport between the different layers, and this increased the overall rate of As release from zones limited by diffusion. Desorption rate of As in the layered system was fast initially, followed by a period of slow desorption rate that lasted months. The desorption hysteresis was due to slow desorption controlled by diffusion. The results provide important insights for understanding and modeling As desorption and transport in field systems.