Irgarol 1051 and Diuron are used as boosters in copper-based anti-fouling paints, as well as in agriculture and home gardening. We monitored the coral reefs and adjacent waters of northern Okinawa Island three times, i.e., in August 2015, June 2016 and December 2016. The mean concentrations were 1.44 ng/L for Irgarol and 1.07 ng/L for Diuron. Although the range of these concentrations was lower than those previously recorded in southern Japan, Irgarol and Diuron were significantly higher in December 2016 than in June 2016. Several estimations of Predicted No Effect Concentrations (PNECs) have recently been published. In December 2016, compared to the lowest PNEC concentration of each substances, the concentrations of Irgarol and Diuron exceeded the PNEC at nine sites and three sites, respectively. These results suggest that the effects of low concentrations of Irgarol and Diuron, close to the PNEC, on hermatypic corals need to be investigated. The regulation of anti-fouling paints in Japan is self-regulated through industry cooperation. Irgarol and Diuron have not been registered as anti-fouling paints for fishing nets by the fishing cooperatives. The significant increase of these substances suggests that the activity of vessels with paints containing Irgarol has increased in December 2016. This study highlights the need for continuous monitoring of these herbicides in coral reefs and adjacent waters.