Untreated wastewater released into rivers can result in water pollution, the spread of waterborne diseases, harm to ecosystems, contamination of soil and groundwater, as well as air pollution and respiratory problems for nearby humans and animals due to the release of greenhouse gases. The current study aims to investigate the recent input of anthropogenic loads into the rivers using linear alkylbenzene (LAB), which is one of the molecular chemical markers with application of sophisticated model statistical analyses. In order to determine the compositions of LABs, which act as wastewater pollution molecular indicators, surface sediment samples from the Muar and Kim Kim rivers were collected. Gas chromatography-mass spectrometry (GC-MS) was utilized to identify LABs and investigate their sources and degradation. ANOVA and the Pearson correlation coefficient were employed to determine the significance of differences between sampling locations, with a threshold of p < 0.05. To assess the degradation degree and efficacy of wastewater treatment plants (WWTPs), LABs were identified based on chains ranging from long to short (L/S), C13/C12 homolog, and internal to external (I/E) congeners. The results indicated that LAB concentrations in the studied areas of the Muar River ranged from 87.4 to 188.1 ng g−1dw. There were significant differences in LAB homology at p < 0.05, and a significant percentage of sampling stations contained C13-LAB homology. Based on the LAB ratios (I/E) determined, which ranged from 1.7 to 2.2 in the studied areas, it was concluded that effluents from primary and secondary sources are being discharged into the marine ecosystem in those areas. The degradation of LABs was up to 43% in the interrogated locations. It can be inferred that there is a requirement for enhancing the WWTPs, while also acknowledging the efficacy of LAB molecular markers in identifying anthropogenic wastewater contamination.