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The impact of long-term exposure (6 months) to highly or slightly polluted sediments on the energy metabolism of an ecosystem engineer (the oligochaete Limnodrilus hoffmeisteri) was investigated in laboratory conditions. We evaluated some mitochondrial parameters (respiratory chain activity and ATP production rate) and the accumulation of anaerobic end-products (lactate, alanine, succinate, and propionate). The sediments were collected from stormwater infiltration basins and presented high levels of heavy metals and polycyclic aromatic hydrocarbons (PAHs). These compounds had been drained by the runoff water on impervious surfaces of urban areas during rainfall events. A decrease in the activity of the mitochondrial electron transport chain was observed in worms exposed to the most polluted sediment. Urban contaminants disrupted both aerobic metabolism and mitochondrial functioning, forcing organisms to shift from aerobic to anaerobic metabolism (which is characteristic of a situation of functional hypoxia). Although L. hoffmeisteri is very tolerant to urban pollutants, long-term exposure to high concentrations can cause disruption in mitochondrial activity and therefore energy production. Finally, this study demonstrated that anaerobic end-products could be used as biomarkers to evaluate the impact of a mixture of urban pollutants on invertebrates.