Water and sediment samples were collected from 20 location of the Buriganga river of Bangladesh during Summer and Winter 2009 to determine the spatial distribution, seasonal and temporal variation of different heavy metal contents. Sequential extraction procedure was employed in sediment samples for the geochemical partitioning of the metals. Total trace metal content in water and sediment samples were analyzed and compared with different standard and reference values. Concentration of total chromium, lead, cadmium, zinc, copper, nickel, cobalt and arsenic in water samples were greatly exceeded the toxicity reference values in both season. Concentration of chromium, lead, copper and nickel in sediment samples were mostly higher than that of severe effect level values, at which the sediment is considered heavily polluted. On average 72 % chromium, 92 % lead, 88 % zinc, 73 % copper, 63 % nickel and 68 % of total cobalt were associated with the first three labile sequential extraction phases, which portion is readily bioavailable and might be associated with frequent negative biological effects. Enrichment factor values demonstrated that the lead, cadmium, zinc, chromium and copper in most of the sediment samples were enriched sever to very severely. The pollution load index value for the total area was as high as 21.1 in Summer and 24.6 in Winter season; while values above one indicates progressive deterioration of the sites and estuarine quality. The extent of heavy metals pollution in the Buriganga river system implies that the condition is much frightening and may severely affect the aquatic ecology of the river.