The focus of this study, carried out on mudflat and mangrove sediments of Ulhas Estuary and Thane Creek in Mumbai, India, documents how sediment analysis in different ecosystems can help in understanding metal behaviour and pollution status of the region. Based on the the geoaccumulation index (I _geo ), the study shows that the estuarine and creek regions, being recipients of industrial and domestic wastes, display moderate pollution. Ulhas Estuary with higher clay and organic matter contents, exhibits higher amounts of metals than Thane Creek. Furthermore, using correlation and cluster analyses, the creek projects stable subenvironments with similar types of metal associations, with Fe and total organic carbon as the dominant metal carriers. By contrast, in the estuarine subenvironments, the metal associations do not reveal any distinct trend, which may be attributed to the disturbance caused by dredging activities routinely carried out in the region. Factor analysis carried out on I _geo data in both regions further helped in identifying polluted metal groups.