Industrial wastewaters are recognized as a valuable resource, however, their disposal without proper treatment can result in environmental deterioration. The associated environmental/operational cost of wastewater treatment necessitates upgrade of applied processes towards the goals of sustainability and mitigation of climate change. The implementation of cyanobacteria-based processes can contribute to these goals via resources recovery, production of high-value products, carbon fixation and green-energy production. The present study evaluates the cyanobacterium Synechococcus elongatus PCC 7942 (S7942) as a biological component for novel and sustainable alternatives to typical biological nutrient removal processes. Valuable results regarding cultivation temperature boundaries, applied disinfection techniques and analytical methods, as well as regarding relations between parameters expressing S7942 biomass concentration are presented. The results show that at typical industrial wastewater temperatures, S7942 efficiently grew and removed nitrates from treated snack-industry's wastewater. Moreover, in cultures with treated and relatively saline dairy wastewater, its growth rate slightly decreased, but nevertheless nitrates removal rate remained efficiently high. A comparison between typical denitrification processes and the proposed nutrient removal process indicated that a S7942-based system may constitute an alternative or a supplementary to denitrification process. Thus, Synechococcus elongatus PCC 7942 proved to be a potent candidate towards sustainable industrial wastewater treatment applications.