The complexity of water contaminants, both chemical and biological requires an efficient and feasible treatment alternative. Herein, the photocatalytic ozonation treatment using graphitic carbon nitride catalysts was effectively applied for the elimination of a mixture of targeted chemical contaminants, and both Escherichia coli bacteria and Human polyomavirus JC (JC virus) in real secondary wastewater. The exfoliation treatment was compared in catalysts prepared using urea and melamine as precursors. The physical treatment provided no significant enhancement in the urea-based catalyst, while the improvement in the structure of the melamine-based (36MCN) material and formation of melem heterojunction increased its catalytic properties. In both sets of contaminants, the photocatalytic ozonation systems were superior to photolytic ozonation, especially regarding ozone consumption. The best catalyst, 36MCN, resulted in a decrease of 57.5%, 33.0% and 29.0% in the ozone dose required to eliminate chemical, bacteria and virus contaminants, respectively. The hydroxyl radicals were also shown as a key responsible for the pollutant’s elimination. The higher radical production and decomposition of ozone are possible indications of the better performance of graphitic carbon nitride photocatalytic ozonation, as an efficient tertiary wastewater alternative.