This chapter provides an introduction to the structure, the sources, and the harm to the human body of persistent toxic substances (PTSs) in aquatic environment, which includes some organic substances and heavy metal ions that can be detected using electrochemical analysis. Persistent Organic Pollutants (POPs) are mainly hydrocarbons that can be directly released into aquatic ecosystems during the process of production and use of industrial products. The chapter explains in detail several common POPs: polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), polycyclic aromatic hydrocarbons (PAHs), hydrazines, and mercaptans. As for the inorganic pollutants, heavy metal ions should be mentioned as PTS pollutants. Nowadays, incidents of heavy metal contamination in aquatic environment are continuously emerging and attract increasing attention. Considering the harmful extent and distribution of heavy metal ion pollution, pollution due to lead, mercury, cadmium, chromium, arsenic, zinc, silver, cobalt, and nickel ions are discussed in the chapter.