This study investigated the efficiency of a microwave-enhanced Fenton Advanced Oxidation Process (Fe2+/H2O2, pH 2.5-3.5, 700 W, 70°C, 10 min) as a tertiary treatment strategy for degrading emerging organic contaminants in industrial effluents. The treatment involved a 30-minute pre-stirring phase (20 min equilibration with Fe2+, 10 min mixing with H2O2 prior to 10 minutes of microwave irradiation. Twenty complex wastewater samples were collected from pharmaceutical, healthcare, and simulated cosmetic systems across Kano and Kaduna States, Nigeria. Physicochemical parameters and Gas Chromatography-Mass Spectrometry (GC-MS) profiles were evaluated before and after treatment. Untreated effluents exhibited heavy pollution, with baseline chemical oxygen demand (COD) ranging from 1000 to 5300 mg/L, high coliform counts, heavy metals, elevated hardness (Ca2+/Mg2+), and phenolic activity. Post-treatment COD reductions reached 10.0% to 85.0%, with highest removal in Methylated Spirit (85.0%) and Boric Acid (82.4%) streams, while mineral-dense softener brine yielded 10.0%. Initial zero-BOD values were transformed into biodegradable fragments, coliforms were rendered undetectable, and initial heavy metals, hardness, and phenolic activity were remediated. GC-MS resolved 223 organic compounds in raw effluents, including Diphenhydramine (39.8%), DEHP (5.1–10.9%), DBP (8.0–20.0%), and Octocrylene. Post-treatment chromatography confirmed 55% to 100% removal for the majority of tracked pharmaceutically active compounds, personal care products, and endocrine-disrupting chemicals. These findings demonstrate the technical viability of localized advanced oxidation technologies and provide empirical baseline data to inform regulatory discharge standards in low- and middle-income settings.