Nowadays, increasing attention is focused on the indirect impacts of emission control technologies and the potential burden shifting. A clear example is the generation of wastewater when wet scrubbing systems are used for flue gas cleaning. The present study takes into consideration a typical wet scrubber for waste-to-energy plants and the available options for wastewater management: physicochemical treatment, evaporation or valorisation. A comparative assessment of the environmental footprint of the alternatives is performed by taking into account the burdens related to the supply of reactants, energy and the disposal of process residues (solid and liquid waste streams). It is thus shown that the recovery of a marketable product from the effluent produces a net environmental benefit, while the choice between wastewater discharge or evaporation represents only a shift of burden between the water and the soil compartments.