The present study evaluates the removal of micropollutants from water/wastewater contaminated sources through the application of a heterogeneous catalytic ozonation process, using a pilot-scale continuous operation unit, composed of a membrane module for the diffusion and effective dilution of ozone into the liquid phase to be treated and a plug flow reactor/continuous stirred tank reactor (PFR/CSTR) contact reactor system in series, where the catalyst is recirculated in dispersion mode. The solid materials tested as catalysts are natural and calcined zeolite, Bayoxide and alumina, whereas the examined micropollutants, used in this case as probe compounds, are p-chlorobenzoic acid (p-CBA), atrazine, benzotriazole and carbamazepine. A high-performance liquid chromatography system was used to determine the removal of micropollutants. In the case of p-CBA, an ozone-resistant compound, the addition of catalyst was found to significantly enhance its degradation rate, leading to >99% removal under the optimum defined conditions, i.e., in terms of catalyst concentration, pH, temperature, and process time. On the other hand, in the case of atrazine, a different ozone-resistant compound, the introduction of examined catalysts in the ozonation process was found to reduce the degradation of micropollutant, when compared with the application of single ozonation, indicating the importance of specific affinity between the pollutant and the solid material used as catalyst. Benzotriazole, a moderately ozone-reactive compound was degraded by more than 95% under all experimental conditions and catalysts tested in the pilot unit, while carbamazepine, a highly ozone-reactive compound, was completely removed even during the first stage of treatment process (i.e., at the membrane contactor). When increasing the pH value (in the range 6–8) and the contact time, the performance of catalytic ozonation process also improved.