The presence of diverse pollutants in water has been threating human health and aquatic ecosystems on a global scale. For more than a century, chemical oxidation using strongly oxidizing species was one of the most effective technologies to destruct pollutants and to ensure a safe and clean water supply. However, the removal of increasing amount of pollutants with higher structural complexity, especially the emerging micropollutants with trace concentrations in the complicated water matrix, requires excessive dosage of oxidant and/ or energy input, resulting in a low cost-effectiveness and possible secondary pollution. Consequently, it is of practical significance but scientifically challenging to achieve selective oxidation of pollutants of interest for water decontamination. Currently, there are a variety of examples concerning selective oxidation of pollutants in aqueous systems. However, a systematic understanding of the relationship between the origin of selectivity and its applicable water treatment scenarios, as well as the rational design of catalyst for selective catalytic oxidation, is still lacking. In this critical review, we summarize the state-of-the-art selective oxidation strategies in water decontamination and probe the origins of selectivity, that is, the selectivity resulting from the reactivity of either oxidants or target pollutants, the selectivity arising from the accessibility of pollutants to oxidants via adsorption and size exclusion, as well as the selectivity due to the interfacial electron transfer process and enzymatic oxidation. Finally, the challenges and perspectives are briefly outlined to stimulate future discussion and interest on selective oxidation for water decontamination, particularly toward application in real scenarios.