This study investigates the occurrence, phase partitioning, and source apportionment of sixteen priority polycyclic aromatic hydrocarbons (PAHs) across the surface water and sediment interface of the Can Tho River network, a rapidly urbanizing hub in the Vietnamese Mekong Delta. Analysis of samples from nineteen sites revealed a distinct phase fractionation mechanism governing PAH distribution. The aqueous compartment was dominated by low-molecular-weight (LMW) congeners, specifically acenaphthylene and acenaphthene, which exhibited significant positive correlations with biodegradable organic matter (BOD5, COD), indicating a co-transport mechanism driven by domestic effluents and urban runoff. Conversely, bottom sediments functioned as a preferential sink for high-molecular-weight (HMW) and carcinogenic compounds (e.g., benzo[b]fluoranthene, indeno[1,2,3-cd]pyrene), reflecting their strong hydrophobic affinity for the sedimentary matrix. Spatial analysis delineated a clear urban-rural dichotomy: urban and traffic-intensive zones were characterized by elevated pyrogenic signatures linked to vehicular emissions and inland waterway transport, whereas agricultural areas displayed a stable petrogenic background. Diagnostic ratios further corroborated petroleum combustion as a primary contributor to the sedimentary burden. Although aggregate concentrations remained within national and international safety thresholds, the specific enrichment of persistent HMW PAHs in the urban core signals an emerging ecological risk. These findings underscore the critical role of urbanization and organic matter dynamics in modulating pollutant fate, providing an essential baseline for environmental management in tropical deltaic systems.