In this study, the distributions and sources of sediment-associated polycyclic aromatic hydrocarbons (PAHs) and hopanes in the Malaysian rivers and estuaries were evaluated. The concentrations of 16 USEPA PAHs varied from 225.5 to 293.9 (Perlis River), 195.2 to 481.2 (Kedah River), 791.2 to 1995.4 (Merbok River), 231.2 to 426.7 (Perak River), and 3803.2 to 7442.7 ng g(-1) (Klang River) dry weight. PAHs can be classified as moderate in the Perlis, Kedah, and Perak Rivers, moderate to high in the Merbok River, and high to very high in the Klang River. The comparison of PAHs with sediment quality guidelines (SQGs) indicates that occasionally adverse biological effects may occur from total PAHs, low molecular weight (LMW), and high molecular weight (HMW) PAHs at stations 1, 2, and 3 of the Klang River and from total PAHs at station 2 of the Merbok River. The diagnostic ratios of individual PAHs indicate both petrogenic and pyrogenic origin PAHs with significant dominance of pyrogenic sources in the study areas. The results suggest that Malaysian sediments had hopane ratios (C29/C30) similar to MECO suggesting MECO as a major source of the petroleum hydrocarbons found in the sediments, which is consistent with results reported in previous studies. These findings demonstrate that effective and improved environmental regulations in Malaysia have shifted the source of petroleum hydrocarbons from petrogenic to pyrogenic origin.