Aquatic environments are among the most noteworthy ecosystems regarding chemical pollution due to the anthropogenic pressure. In 2000, the European Commission implemented the Water Framework Directive, with the aim of progressively reducing aquatic chemical pollution of the European Union countries. Therefore, the knowledge about the chemical and ecological status is imperative to determine the overall quality of water bodies. Concerning Portugal, some studies have demonstrated the presence of pollutants in the aquatic environment but an overall report is not available yet. The aim of this paper is to provide a comprehensive review about the occurrence of priority substances included in the Water Framework Directive and some classes of emerging organic pollutants that have been found in Portuguese aquatic environment. The most frequently studied compounds comprise industrial compounds, natural and synthetic estrogens, phytoestrogens, phytosterols, pesticides, pharmaceuticals and personal care products. Concentration of these pollutants ranged from few ng L(-1) to higher values such as 30 μg L(-1) for industrial compounds in surface waters and up to 106 μg L(-1) for the pharmaceutical ibuprofen in wastewaters. Compounds already banned in Europe such as atrazine, alkylphenols and alkylphenol polyethoxylates are still found in surface waters, nevertheless their origin is still poorly understood. Beyond the contamination of the Portuguese aquatic environment by priority substances and emerging organic pollutants, this review also highlights the need of more research on other classes of pollutants and emphasizes the importance of extending this research to other locations in Portugal, which have not been investigated yet.