Groundwater-sourced drinking water quality in South Asia, specifically India, is extremely stressed, mostly from the presence of many pervasive and geogenic pollutants. The presence and behavior of anthropogenic pollutants like polycyclic aromatic hydrocarbons (PAHs) are poorly investigated on a regional or basin-wide scale. The present study provides one of the first documentation of the presence and behavior of PAH in the aquifer sediments in the Ganges river basin. Lower and medium molecular weight PAHs, e.g., naphthalene, phenanthrene, and fluoranthene were detected in 79, 36, and 13% of samples ( = 25). The PAH level in groundwater was approximately five times lower than river water. The sorption behavior of PAHs were studied in experiments in presence/absence of organic carbon and by simulating advective transport of low to medium molecular weight PAHs, e.g., naphthalene, phenanthrene, and fluoranthene in aquifer sediments collected from agricultural, peri-urban, and urban areas. Naphthalene and phenanthrene adsorbed on quartz and kaolinite, but not on clay minerals like kaolinite. Fluoranthene adsorbed more favorably on kaolinite. Numerical modeling of the advective transport of PAHs in aquifers suggest up to 25 times faster movement of pollutants from irrigation-induced pumping, indicating the strong control of hydraulics on the spatial distribution of PAHs in subsurface.