Estuarine environment is complex and receives different contaminants from numerous sources that are persistent, bioaccumulative and toxic. The distribution, source, contamination and ecological risk status of heavy metals in sediment of Brisbane River, Australia were investigated. Sediment samples were analysed for major and minor elements using LA-ICP-MS. Principal component analysis and cluster analysis identified three main sources of metals in the samples: marine sand intrusion, mixed lithogenic and sand intrusion as well as transport related. To overcome inherent deficiencies in using a single index, a range of sediment quality indices, including contamination factor, enrichment factor, index of geo-accumulation, modified degree of contamination, pollution index and modified pollution index were utilised to ascertain the sediment quality. Generally, the sediment is deemed to be “slightly” to “heavily” polluted. A further comparison with the Australian Sediment Quality Guidelines indicated that Ag, Cr, Cu, Ni, Pb and Zn had the potential to rarely cause biological effects while Hg could frequently cause biological effects. Application of potential ecological risk index (RI) revealed that the sediment poses moderate to considerable ecological risk. However, RI could not account for the complex sediment behaviour because it uses a simple contamination factor. Consequently, a modified ecological risk index (MRI) employing enrichment factor is proposed. This provides a more reliable understanding of whole sediment behaviour and classified the ecological risk of the sediment as moderate to very high. The results demonstrate the need for further investigation into heavy metal speciation and bioavailability in the sediment to ascertain the degree of toxicity.