Sediment is an important part of an aquatic ecosystem, so it is essential to develop an effective sediment quality assessment tool. This study aims to develop a new sediment quality assessment tool using a Weight of Evidence approach in combination with the grey TOPSIS (Technique for Order Preference by Similarity, a mathematical calculation of multi-criteria decision analysis). This tool can analyze data from chemical analyses, laboratory toxicity tests and benthic community structure analyses to generate individual results from each line of evidence, and integrate data from these three lines of evidence to obtain an overall assessment through an Excel Visual Basic for Application program. The tool can compare the relative magnitude of risks among sites and rate each site with high, moderate, or low ecological risk, thus guiding us to take pertinent measures toward polluted sediment. A case study of the sediment of Dongjiang River basin, south China, demonstrated the successful application of this tool. It proved that this assessment tool can provide a comprehensive and accurate assessment of sediment quality and efficiently discriminate risks among different sites, suggesting it is a powerful tool for environment risk assessment.