The concentrations of Ca, Mg, K, Zn, Pb, Cd, Co, Cr, Cu, Fe, Ni and Na were determined in the sediment and biota of the Bonny/New Calabar River Estuary in Niger Delta, Nigeria using atomic absorption spectrophotometer A-100. The concentration of the respective metals varied between 2011 and 2012. The range of mean values are presented in mg/kg along with variations at a statistically significant level (P < 0.05). In sediment, only Cr varied significantly (p < 0.05) within the two years. Bioaccumulation factor (BF) indicated a more potent source of metals from sediment than biota, accumulating Zn, Fe and Ni in magnitudes 10, 6 and 5 times more, respectively. The study shows elevated levels of heavy metals in sediment and bioaccumulation in biota. Regular monitoring and comparison of results with World Health Organization maximum permissible limits should be carried out, in order not to allow the metal concentration to reach alarming levels.