Agro-industrial wastewater, rich in nutrients and organic matter, represents both an environmental challenge and a valuable resource for biomass valorization. This study assessed the formation, functional performance, and compositional quality of microalgal–bacterial aggregates (MBAs) cultivated exclusively in agro-industrial wastewater under different hydrodynamic conditions. Open photobioreactors operated at 50 and 100 rpm were used to promote aggregate development, followed by closed static and dynamic batch operations to evaluate contaminant removal efficiency. The systems achieved high pollutant removal rates, including 98% ammonium, 95% phosphate, 65–80% Chemical Oxygen Demand (COD), and complete elimination of E. coli, while moderate agitation enhanced aggregation and settleability without compromising treatment efficiency. Dynamic operation maintained more stable removal performance and biomass retention compared to static systems. The recovered biomass exhibited a favorable nutritional profile (12.5% protein, 4.39% lipids, and 31% dietary fiber) and tested negative for cyanotoxins and pathogens, confirming its microbiological safety. Overall, the findings demonstrate that MBAs cultivated from agro-industrial wastewater can effectively couple bioremediation with the production of safe, nutrient-rich biomass, offering a sustainable and circular solution for wastewater management and bioresource recovery.