In this work, a simple g-C3N4 quantum dots enriched MoO3 nanohybrid was formulated for the synergistic photocatalytic degradation of an industrially active organic pollutant, p-chlorophenol (PCP) and a widely prescribed antibiotic, rifampicin (RIF). The nanohybrid was synthesised via a facile ultrasonic assisted hydrothermal method and characterized using various characterization analysis. The efficient Z-scheme charge transfer of the nanohybrid resulted in the elimination of 98% PCP and 89% RIF under visible light with a rate constant of 0.012 and 0.006 min−1 respectively. The photocatalysis was attributed to the formation of both hydroxyl (OH•) and superoxide (O2•-) radicals in the resulting nanohybrid. The intermediates formed in the course of reaction were estimated through gas chromatography-mass spectroscopy/mass spectroscopy (GC-MS/MS) analysis and a suitable degradation pathway was constructed. The structural stability and reusability of the nanohybrid was affirmed through X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) analysis to outweigh the industrial potential of the catalyst, with 85% PCP and 80% RIF removal efficiency after six cycles of degradation. In addition, the mineralization of the pollutants was confirmed by total organic carbon analysis. Further, the toxicity of the drug and the formed intermediates was determined using ecological structure activity relationships (ECOSAR) software. On the whole, this work provides an excellent insight for the development of environment-friendly materials in a large scale for the degradation of water-based pollutants.