In this study, variation of total heavy metal concentrations in the bed sediments against the flow rate of the lower Seyhan river has been evaluated. Sediment samples were collected at 6 representative sampling stations along the lower Seyhan river, Turkey under low and high flow conditions during four seasons. Concentrations of Cd, Cu, Fe, Mn, Ni, Pb and Zn decreased by increasing river flow rate. Sediment quality assessment according to the "U.S.EPA Sediment Quality Guidelines (SQG)" revealed that there was heavy metal pollution with respect to especially Ni, Cd and Zn. However, mean Cu and Pb levels in the river indicated that the river was non-contaminated. There were several mechanisms suggested for heavy metal distribution in the river such as immobilization by sedimentation, remobilization by pH decrease due to microbial degradation of organic matter and resuspension due to increased river flow rate.