Micropollutants and emerging substances pose a serious problem to environmental sustainability and remediation, due to their widespread use and applications in everyday life. This group of chemicals is diverse but with common toxic and harmful properties. Their concentration in the environment is often very low; however, due to their recalcitrant nature, they are persistent in air, water, and soil. From an engineering point of view, the challenge is not straightforward. It is difficult to remove these contaminants from complex mixtures of substances by conventional methods used in wastewater and drinking water treatment. Ozonation and ozone-based AOPs are accepted processes of degradation of resistant substances or at least enhancement of their biodegradability. The aim of this review paper is to present research trends aimed at solving problems in the research and application of ozone-based processes in the removal of micropollutants from wastewater, thus preventing leakage of harmful substances into surface water, soil, and groundwater and facilitating the reuse of wastewater. Priority substances, micropollutants and emerging pollutants, as well as processes and technologies for their transformation and elimination, are briefly specified. Results obtained by the authors in solving research projects that were aimed at eliminating selected micropollutants by ozonation and ozone-based AOPs are also presented. This review focuses on selected alkylphenols, petroleum substances, and organochlorine pesticides.