Risk assessment was carried out to determine the compatibility of dredged sediments contaminated by mercury with the disposal in a confined structure, to be used as a wharf. Different risk assessment procedures were applied based on the utilization both of total concentration data and of speciation data input and on different transport models. Different strategies of disposal within the confined structure were tested too. A detailed site-specific modeling approach showed the best implementation of risk assessment. In particular, mercury speciation data and the application of three-layer finite system transport model were used. The limitations of the traditional models, even with some improvements proposed by literature, have been stressed in comparison with the proposed three-layer finite system transport model. The raising awareness in the advantages of a detailed site-specific investigation, modeling and consequently risk assessment leads to a more sustainable choice for a site-specific solution. On the other hand, this proposal follows European Union Strategies about waste prevention and recycling in the context of sustainable use of resources; alternatively, polluted sediments should be disposed of in dedicated sites such as landfill out of Italy with too much expensive costs and very high risks.