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Prevention and management of water pollution are becoming a great challenge in the present scenario. Different conventional methods like carbon adsorption, ion exchange, chemical precipitation, evaporation, and biological treatments remove water pollutants. Nowadays, the requirement for effective, non-toxic and safe waste management strategies is very high. Nanomaterials have been explored in various fields due to their unique characteristics. Green synthesis of nanomaterial is becoming more popular due to their safety, non-toxicity, and ease of scale-up technology. Metal nanoparticles can be synthesized using a green synthesis method using biological sources provided by eco-friendly, non-hazardous nanomaterials with superior properties to bulk metals. Hence, this study has designed a green synthesis of magnetic (cobalt oxide) and noble (gold) nanoparticles from the fresh flowers of Clitoria ternatea. The flavonoids and polyphenols in the extract decreased the energy band gap of cobalt oxide and gold nanoparticles; hence, the capping of the natural constituents in Clitoria ternatea helped form stable metal nanoparticles. The cobalt oxide and gold nanoparticles are evaluated for their potential for eliminating organic pollutants from industrial effluent. The novelty of this present work represents the application of cobalt oxide nanoparticles in the removal of organic pollutants and a comparative study of the catalytic behaviour of both metal nanoparticles. The degradation of bromophenol blue, bromocresol green, and 4–nitrophenol in the presence of gold nanoparticles was completed in 120, 45, and 20 min with rate constants of 3.7 × 10−3/min, 6.9 × 10−3/min, and 16.5 × 10−3/min, respectively. Similarly, the photocatalysis of bromophenol blue, bromocresol green, and 4–nitrophenol in the presence of cobalt oxide nanoparticles was achieved in 60, 90, and 40 min with rate constants of 2.3 × 10−3/min, 1.8 × 10−3/min, and 1.7 × 10−3/min, respectively. The coefficient of correlation (R2) values justify that the degradation of organic pollutants follows first-order kinetics. The significance of the study is to develop green nanomaterials that can be used efficiently to remove organic pollutants in wastewater using a cost-effective method with minimal toxicity to aquatic animals. It has proved to be useful in environmental pollution management.