To investigate the deteriorating health of coral reefs in Okinawa, Japan, natural sediment samples were analyzed for diuron, Irgarol 1,051, chlorpyrifos, and bisphenol A (BPA) which are hazardous to corals. Samples were analyzed by solid-phase extraction (SPE) followed by high-performance liquid chromatography with tandem mass spectrometry (LC-MS-MS). Although diuron and chlorpyrifos usage is only well recorded for farms and not for cities, these chemicals were detected in both rural and urban areas. Additionally, diuron concentration in urban areas was in some cases higher than in rural areas, which might be caused by greater consumption of these chemicals in home gardens in city areas. Irgarol 1051 was detected in downstream river areas, which are situated far from the source sites such as pier or fishery harbor (0.6-3.2 km). This result suggested that Irgarol 1051 could be transported from the river mouths to the sampling sites during flood tides. High BPA concentrations were associated with urban areas (<1.2-22.0 microg kg(-1)), while low concentrations were associated with rural areas (nd-6.8 microg kg(-1)). The river sediments under study are delivered to coral reefs in large quantity through runoff caused by typhoons and other heavy rains. The highly hazardous chemicals are carried into coral reefs on these sediments. Therefore, these hazardous chemical substances may already be influencing the coral reefs.