Ciprofloxacin is a pharmaceutically active compound which belongs to a class of micropollutants that cannot be removed using conventional water treatment systems. In this study, photocatalytic degradation using materials with high surface area and active sites was proposed to remove such contaminants. We demonstrated an easily scalable and simple synthesis route to prepare a 3D porous sulfur-doped g-CN/ZnO hybrid material, and the preparation process parameters were optimized using response surface methodology targeting Ciprofloxacin degradation. The hybrid material removed up to 98% of the bio-toxic Ciprofloxacin from synthetic water. The porous, defect engineered, thermally stable, and chemically interconnected hybrid material presented an 18 and 38% improved degradation efficiency compared to ZnO and sulfur-doped g-CN (or S-CN), respectively. Based on our experimental results, an empirical relation correlating synthesis process parameters and degradation efficiency was developed using face-centered central composite design (FCCD) and response surface methodology (RSM). The current model can be used to design catalytic materials for removing bio-toxic and other micropollutants from water.