Operational mode of photobioreactor (PBR) play pivotal role in environmentally benign wastewater treatment. In this context, there is wider knowledge gap in decision making for sustainable microalgae PBR operation with least environmental impact. Therefore, the present work utilized two operational modes, aeration and mechanical mixing (non-aeration), for comparative evaluation of their impacts on nutrient removal, microalgae: bacteria (M:B) population dynamics, and performance along with environmental impact. The experiments initiated with dominant M:B inoculation ratio (60:40), demonstrated higher M:B ratio (78:21) with mixing regime, as essential nutrients (dissolved inorganic carbon and ammoniacal nitrogen) were conserved within the wastewater. On the other hand, lower M:B ratio (36:63) was obtained during aeration regime, as these nutrients were transformed into CO2 and NH3 and emitted to the environment. The nutrient conservation mechanism within mixing regime enhanced microalgal growth by 30 %, metal removal by 14–59 %, and exhibited carbon negative global warming potential (-0.0451 kgCO2 eqm−3), along with overall non-negative environmental impact. In contrast, aeration strategy showed net negative environmental impact with reduced contaminant removal potential. Overall, this study reveals a previously overlooked yet significant contribution of nutrient conservation achieved through mixing regime for holistic wastewater treatment.