Small density variations due to low solute concentrations in the stream water commonly exist in streams and rivers. Using laboratory experiments and numerical modeling, we demonstrated that even such small density variations could influence the hyporheic flow in the streambed with the presence of periodic bedforms. The circulating pore water flow patterns in the bed were modified constantly as the solute front moved downward. Density-induced head gradients eventually overwhelmed the regional hydraulic gradient and drove the circulating flow below a hydraulic divide that would have existed without the density influence. The density-modified hyporheic flow provided a relatively fast solute transport mechanism and enhanced the overall mass exchange between the stream and bed. These results highlight the important role of weak, upward density gradients in modulating hyporheic flow.