Organic pollutants have detrimental effects on the environment. In this study we evaluated the current status of contamination with organochlorine pesticides (OCPs), organo-tin compounds (OTCs), and polychlorinated biphenyls (PCBs) in the waters in and around Okinawa Island, Japan. Possible toxicological effects of these pollutants on marine life including corals are also discussed. Concentrations of total OCPs in river water were in the range of 1.02–56.4 ng liter⁻¹. Among the OCPs, α-BHC, β-BHC, and aldrin were common in river water. OTCs detected in 30 samples of seawater were (mean ±SD) monobutyl tin (MBT), 0.44 ±0.75 ng (Sn) liter⁻¹; dibutyl tin (DBT), 1.32 ±2.70 ng (Sn) liter⁻¹; tributyl tin (TBT), 0.72 ±2.90 ng (Sn) liter⁻¹; monophenyl tin (MPhT), 0.04 ±0.42 ng (Sn) liter⁻¹; diphenyl tin (DPhT), 0.007 ng (Sn) liter⁻¹; and triphenyl tin (TPhT), 0.013 ng (Sn) liter⁻¹. Highest concentrations of TBT, 28.5 ng (Sn) liter⁻¹ for water and 172 ng (Sn) g⁻¹ dry weight for sediment, were detected in samples from Itoman Port. Concentrations of total PCBs were 0.05–0.28 ng liter⁻¹ in open ocean and from 1.59 to 2.48 ng liter⁻¹ in coastal waters. Overall, this study shows that the coral reef ecosystems and their adjacent environments around Okinawa Island are contaminated by toxic organic contaminants (OCPs, OTCs, and PCBs). Levels of these contaminants detected in some sites have exceeded the Environmental Quality Target (EQT), which may pose a risk to health of marine life.