In this study, monthly and daily samplings were carried out at Klang, an eutrophic estuary and at Port Dickson, an oligotrophic coastal water system. Escherichia coli concentration was measured via culture method and the phylogenetic structure of Escherichia coli population was via Clermont typing. Average Escherichia coli concentration at Klang was higher than Port Dickson (t = 2.97, df = 10, p < 0.05), and daily sampling did not show any apparent temporal variation at both sites. At Klang, salinity was inversely correlated with coliform (R2 = 0.216, df = 25, p < 0.05), suggesting that river flow was a mode of transport for coliform. Although Escherichia coli concentration was higher at the eutrophic site, Escherichia coli population structure at both Klang and Port Dickson were similar, and showed neither long-term nor short-term variation. This study showed the predominance of commensal groups A and B1 in tropical coastal waters of Peninsular Malaysia.