The use of antifouling paints to the boats and ships is one among the threats facing coastal resources including coral reefs in recent decades. This study reports the current contamination status of diuron and its behaviour in the coastal waters of Malaysia. The maximum concentration of diuron was 285 ng/L detected at Johor port. All samples from Redang and Bidong coral reef islands were contaminated with diuron. Temporal variation showed relatively high concentrations but no significant difference (P>0.05) during November and January (North-East monsoon) in Klang ports (North, South and West), while higher levels of diuron were detected during April, 2012 (Inter monsoon) in Kemaman, and Johor port. Although no site has shown concentration above maximum permissible concentration (430 ng/L) as restricted by the Dutch Authorities, however, long term exposure studies for environmental relevance levels of diuron around coastal areas should be given a priority in the future.