To reduce environmental impact of flue gases, efficient purification technologies are widely adopted and some of them transfer the pollutants to water phase. The liquid effluents from gas cleaning may thus result in water pollution requiring new management processes. This research aims at developing a specific process for the purification of these effluents, focusing on the removal of nitrogen originated by NOx removal via optimized biological denitrification. Other flue gas constituents or industrial waste stream supplementation to support nitrogen removal are used, completing the NOx removal systems without adverse impacts on water and air in a sustainable way. Potential future targets for its implementation could range from ships to pulp mills, waste incinerators and power plants in urban environments. This application aims at improving skills of the doctoral student in multidisciplinary approaches for the sustainable resolution of environmental challenges, especially developing and modelling bioprocesses as well as building networks for future career.