In the context of the European Water Framework Directive, controlled flooding of lowlands is considered as a potential water management strategy to minimise the risk of flooding of inhabited areas. However, due to historical pollution and overbank sedimentation, metal levels are elevated in most wetlands, which can cause adverse effects on the ecosystem's dynamics. Additionally, salinity affects the bioavailability of metals present or imported into these systems. The effect of different flooding regimes and salinity exposure scenarios (fresh- and brackish water conditions) on Cu and Zn accumulation in the oligochaete Tubifex tubifex (Müller, 1774) was examined. Metal mobility was closely linked to redox potential, which is directly related to the prevalent hydrological regime. Flooded, and thus more reduced, conditions minimized the availability of metals, while oxidation of the substrates during a drier period was associated with a rapid increase of metal availability and accumulation in the oligochaetes.