Pharmaceutical manufacturing generates wastewater with unusual contaminant profiles including extraordinarily high ammoniacal nitrogen concentrations (> 12,000 mg/L) and stream-dependent heavy metal speciation patterns not typically documented in literature. This study documents scientific contributions of segregated treatment effectiveness for high-strength pharmaceutical wastewater, providing novel insights into treatment technology selection mechanisms for diverse contaminant profiles. Three segregated wastewater streams (high-COD, high-TDS, and low-TDS) from an active pharmaceutical ingredient manufacturing facility (100–150 KLD capacity) were comprehensively characterized for 42 physicochemical parameters following IS:3025 and APHA 24th Edition standards. Heavy metal speciation across stream types was analyzed using ICP-OES/ICP-MS (IS:3025 Part-65:2022). Segregated multi-train treatment performance was systematically evaluated to quantify removal effectiveness and elucidate mechanistic pathways for contaminant fate across thermal-oxidative and biological treatment processes. Wastewater characterization reveals unusual pharmaceutical manufacturing signatures: ammoniacal nitrogen of 12,272 mg/L constituting 79% of total nitrogen in high-COD stream (indicating ammonia-based process chemistry), stream-dependent heavy metal speciation (nickel concentration 31-fold higher in low-TDS versus high-COD stream), and extreme phosphorus concentrations (1,251 mg/L in high-TDS stream). Segregated treatment investigation demonstrates differential pathway effectiveness: 90% COD removal in high-TDS streams via thermal-oxidative pathways (35,358 to 3,536 mg/L) versus 85% COD removal in low-TDS streams via biological pathways (2,241 to 336 mg/L). All heavy metals remained within CPCB discharge limits with substantial safety margins. Treatment analysis enables pharmaceutical synthesis pathway attribution for observed heavy metal and nitrogen speciation patterns, providing mechanistic understanding of contaminant fate. This case study documents novel scientific contributions to pharmaceutical wastewater treatment science through systematic characterization of unusual high-strength effluent profiles and investigation of segregated treatment effectiveness for technology selection. Findings advance understanding of contaminant-specific treatment design principles and provide baseline data for segregated treatment optimization in pharmaceutical manufacturing under water scarcity constraints.