Irgarol and Diuron are photosystem II inhibitor in agricultural activities and antifouling paint in shipping sector. A study took place at three major ports surround the Peninsular Malaysia was carried out to construct the distribution of both biocides based on the seasonal and geographical changes. Surface seawater samples were collected during November 2011 to April 2012; pretreated using solid phase extraction technique followed by quantification with GC-MS and LC-MS-MS for Irgarol and Diuron, respectively. Generally, the distribution of Irgarol was lowest during November 2011 and highest during April 2012, which is similar pattern was observed at all ports, whereas the distribution of Diuron was rather vague. The increasing pattern of Irgarol from time to time is probably related to its accumulation in the seawater due to the half-life and consistent utilization. Based on the discriminant analysis, the temporal distribution of Irgarol varied at Klang North Port, Klang South Port and Pasir Gudang Port, whereas Diuron was temporally varied only at Kemaman Port. Furthermore, Irgarol was spatially varied during November 2011, whereas Diuron did not show any significant changes throughout all sampling periods. Ecological risk assessment exhibited high risk for Diuron and Irgarol, but however Irgarol should be of concern due to it relatively higher risk as compared to Diuron. Thus, it is recommended that the current Malaysian guideline and regulation of biocides application should be reevaluated and improve to protect the ecosystem, as well as preventing ecological risk to the aquatic environment.