Filamentous fungi and lithotrophic bacteria were used to leach heavy metals from dredged sediments in semi-pilot scale air-lift bioreactors. A preliminary physico-chemical characterization of the sediments comprising a sequential extraction study revealed their high metallic contamination and a predominant association of the metals with sulphides and organic matter. The mobility of heavy metals from sediments was ranked by decreasing order as follows: Mn > Zn > Cd > Cu > Pb. The conditions that favoured the solubilization of heavy metals by filamentous fungi turned out to be also favourable for the activity of the sediment organotrophic bacteria. The latter produced organic acids under temporary hypoxic conditions and resulted in the solubilization of 77% of manganese, 44% of zinc, 12% of copper, and less than 2% of cadmium or lead. In general, the fungal organotrophic treatments were limited to the relatively mobile metals due to the weak nature of the organic acids produced and to their microbial consumption under limited saccharose conditions. The lithotrophic treatments yielded higher solubilization results than the organotrophic experiments. Sulphur resulted in a faster, and for some metals such as copper and cadmium, in better bioleaching results compared with reduced iron or with a combination of reduced iron and sulphur. The bioleaching percentages varied between 72 and 93% for cadmium, copper, manganese and zinc, except for lead because of the poor solubility of lead sulphate. The sediment's lithotrophic bacteria acidified the matrix through sulphur oxidation, and leached both loosely and tightly bound metals.