A laboratory experiment and numerical modeling were used to examine effects of density gradients on hyporheic flow and solute transport under the condition of a solute pulse input to a river with regular bed forms. Relatively low-density gradients due to an initial salt pulse concentration of 1.55 kg m23 applied in the experiment were found to modulate significantly the pore-water flow and solute transport in the riverbed. Such density gradients increased downward flow and solute transport in the riverbed by factors up to 1.6. This resulted in a 12.2% increase in the total salt transfer from the water column to the riverbed over the salt pulse period. As the solute pulse passed, the effect of the density gradients reversed, slowing down the release of the solute back to the river water by a factor of 3.7. Numerical modeling indicated that these density effects intensified as salt concentrations in the water column increased. Simulations further showed that the density gradients might even lead to unstable flow and result in solute fingers in the bed of large bed forms. The slow release of solute from the bed back to the river led to a long tail of solute concentration in the river water. These findings have implications for assessment of impact of pollution events on river systems, in particular, long-term effects on both the river water and riverbed due to the hyporheic exchange.