Controlled flooding of lowlands is considered as a potential water management strategy to minimize the risk of flooding of inhabited areas during high water periods. However, due to industrial activities, river water, sediments and soils are often contaminated with metals which may have adverse effects on the ecosystem's structure and functioning. Additionally, salinity may greatly affect the bioavailability and toxicity of metals present or imported into these systems. The effect of contaminated soils under different flooding and salinity exposure scenarios on the growth, reproduction and metal accumulation in the oligochaete Tubifex tubifex (Müller, 1774) were examined. In these bioassays metal contaminated soils were flooded with water of different salinities (0 and 3 psu), and tested after 0, 6 and 12 months of permanent inundation. We indeed found that inundation time had significant decreasing effects on Cu and Zn accumulation; although initial accumulation of Cu and Zn was higher in the previously unflooded soil at the start of the flooding treatment, these differences seem to disappear after 6 months of permanent inundation. Moreover, the complex interaction between substrate type and salinity suggests that redox potential is probably of major importance.