This study explores the bioremediation potential of indigenous industrial microalgal consortia for the simultaneous removal of ciprofloxacin (CIP) and nitrate from high-strength pharmaceutical wastewater. Native microalgae were isolated from effluent sources and cultivated in batch reactors for eight days under three conditions: pharmaceutical wastewater (WW), distilled water (DW), and nitrate-rich BG-11 medium. Remarkably, CIP removal reached 85% in WW, 70% in DW, and 57% in BG-11, demonstrating the consortia’s adaptability across different environments. In the BG-11 system, microalgae achieved 78% nitrate removal. However, elevated nitrate levels initially delayed CIP degradation, suggesting competitive interaction during uptake and metabolic processing. These findings reveal that native microalgal consortia can efficiently reduce pharmaceutical pollutants and nutrient loads without the need for genetic modification or external additives. This low-cost, eco-friendly approach offers promising prospects for integrating microalgae into tertiary treatment systems for pharmaceutical effluents, contributing to sustainable wastewater management and environmental protection.