The concentrations of the herbicide Diuron and algaecide Irgarol in the Seto Inland Sea, Japan, were assessed for October 2008 and October 2009. Overall, 29 seawater, sediment and plankton samples were collected from off-shore areas around the sea. The Diuron levels were 0.01-0.062 μg/L, 0.01-0.09 μg/g dry weight (dw) and 0.075-0.45 μg/g dw in seawater, sediments and planktons respectively. Irgarol levels were 0.011-0.055 μg/L, 0.011-0.068 μg/g dw and 0.02-0.36 μg/g dw in seawaters, sediments and planktons respectively. This is the first study to report the presence of Diuron and Irgarol in plankton from aquatic environments. The concentrations of Diuron and Irgarol were similar in both years and the highest levels of concentration were found near the coastal area of Osaka bay, second largest metropolitan region in Japan. The distribution of Diuron and Irgarol in seawaters, sediment and plankton would be largely determined by riverine discharge or uses of these pesticides as antifouling agent at harbors and ports and then transport to offshore from coastal waters by water flows.