The spatial and temporal variability in concentrations of heavy metals, and the portion of the bioavailable metals for bacterial community of Ismailia Canal sediment were conducted. Furthermore, Fourier Transform Infrared Spectroscopy (FTIR) was employed to elucidate the molecular structure of the same sediment samples. Results indicate that Cu, Cr and Zn concentrations showed temporal variation (p<or=0.05). However Pb and Zn showed significant spatial variation (p<or=0.05). Also, the mean value of Pb and Zn in sediment is higher than the shale reference value. There were no temporal or spatial significant in the total viable bacterial count (TVBC) for all sites while Zn shows the highest affinity for bacterial uptake followed by Ni>Pb>Cu>Cr>Co. Also, the shift in the CO suggested that hydrated divalent metals are interacting with organic acids to form hexahydrated metals carboxylate. There were non-significant interactions between temporal and spatial variation for all the studied metals.