In this present study, concentrations of copper and lead were investigated in natural sediment at three locations along the Niger River in Lokoja, Nigeria.  In addition, the ability of bed sediment to control metal ion contamination in aquatic systems through absorption as a sink process was also evaluated. Parameters and models that control the behaviour of metals in solution, such as pHzpc, pH of the sediment,  kinetics, and equilibrium isotherms were interpreted. The pH value of sediment in water and calcium chloride (CaCl2) was in 4.6-7.2 range, indicating that the sediment is moderately acidic and indicating the slow movement of metal ions to overlying water column. The tolerance of River Niger to metal adsorption in the sediment was in the order of Cu<Pb. According to thermodynamic adsorption data, equilibrium isotherms and kinetic studies, the adsorption behaviour of Cu(II) and Pb(II) ions in aqueous solutions occurs spontaneously, and follows Langmuir and Freundlich isotherms, and has a pseudo-first-kinetic order. The current copper (18.81-34.68 mg/kg) and Lead (14.81-38.36 mg/kg) content in Niger River sediment samples are relatively low compared to other river sediments an indication of low anthropogenic activities in the study area.