The economy and population in Taiwan grew rapidly in the 20th century, during which time little attention was paid to marine environmental protection. Discharges of heavy metals, BOD, COD, organic/inorganic nitrogen, and phosphorous have, as a result, caused environmental problems. Besides pollutants brought by long-range transport such as dust storms, haze, and water-borne radiation, locally sourced pollutants were transported to the coastal area by small mountain rivers on the narrow island. This has become a great problem for the coastal environment and a threat to both riverine and coastal organisms. Knowledge about these anthropogenic substances has been increasing due to improved analytical technology and concern has been increasing due to the adverse health effects that are being identified. Therefore, polycyclic aromatic hydrocarbons, radioactive substances, and many emerging contaminants have become new targets for investigation in recent years in the coastal areas where they end up. Their potential risks to the ecosystems have been confirmed, but there are still no relevant regulations for their prevention. Furthermore, there will be more new chemicals that will cause concern in the future. This chapter focuses on these issues as well as on several contaminants that should be investigated further in Taiwan's coastal environment.