Port-dredging activities produce large volumes of contaminated sediments. Dredged sediments are considered a waste by national laws, but recently the desire to consider them a resource has become widespread and remedies for their contamination are being searched to allow their reuse. In this work, we studied, developed, and tested a method for remediate marine-dredged sediments contaminated by heavy metals using native fungi and a microporous membrane, in order to achieve the sediment quality and allow their reuse. Activity was carried out on port sediments from Genoa, Leghorn, Pisa, and Cagliari (Italy). Autochthonous fungi were isolated from each sediment and employed in mycoremediation tests. Two plastic boxes were prepared (for each Port) with 5 kg of sediment in each box, employed for metal bioaccumulation using a sterile polyester membrane inoculated with fungi. Membranes were analyzed at 15, 30, and 60 days after inoculums, and sediments were analyzed after 60 days at the end of the experiment to verify metal contamination degree. Recovery efficiency (RE%) and difference recovery efficiency (DRE%) were calculated for each experiment: the first shows the absorption capability of the membrane-fungi consortium; the second evidences only the fungal contribution to the metal absorption. To assess sediment contamination before and after the mycoremediation treatment, we considered chemical levels of reference L1 (the lowest chemical level of reference) and L2 (the highest chemical level of reference), and the evaluation of chemical hazard (HQ) for the chemical contaminants defined by the Italian Ministerial Decree 173/2016. Fungi from Genoa sediments increase the membrane absorption of Cu and Zn. Regarding Leghorn results, RE (%) increases and reaches the maximum value after 60 days of treatment for each considered metal. Cr tot, Ni, and Mn appear to be hyper-bioaccumulated. DRE values of Pisa sediments show that Mn is excluded by fungi and it does not bioaccumulate, while other metals and in particular Cd, Cr tot, Zn, and Sb are bioaccumulated. Cagliari DREs show that fungi are not able to bioaccumulate Cr tot, Ni, and Mn and their accumulation is due to the membrane, while As and Cd are bioaccumulated. Our work evidenced that selected fungi are able to grow on a microporous support and actively reduce metal concentrations in the sediments, achieving their quality. This biomembrane system may represent an important instrument for the remediation of the residual metal contamination of port sediments.