Abstract The spatial distribution, source identification and ecotoxicological impact of a group of persistent organic pollutants (POPs: dichlorodiphenyltrichloroethane (DDT), hexachlorocyclohexanes (HCHs), polychlorobiphenyls (PCBs), polychlorobenzenes (PCBzs)), and polyaromatic hydrocarbons (PAHs) were investigated in surface sediment samples (0–5 cm, <63 μm grain size) along the ecologically stressed Hooghly River estuary, East India. The results demonstrated a wide range of concentrations (ng/g dry weight) with the following decreasing order: ∑ 16 PAHs (3.3–630) > ∑ 6 DDTs (0.14–18.6) > ∑ 7 PCBs (0.28–7.7) > ∑ 2 PCBzs (0.01–1.3) > ∑ 5 HCH (0.10–0.6), with a dominance of p,p ′-DDT and higher molecular weight PAHs. Selected diagnostic ratios indicated a mixture of both pyrolytic and petrogenic sources of PAHs, inputs of weathered DDT and their degradation in oxidizing environment, and a predominance of industrial input over the agricultural wastes. The cumulative impact of the pollutants (effective range medium quotient (ERMq): 0.01–0.16) reflected minimal to low ecotoxicological risk, with highest probability of toxic effects towards surrounding biota at Barrackpore (21%). ∑ 6 DDTs exceeded the effect range low value resulting occasional adverse impact to the sediment dwelling organisms. Among the PAHs, the 4-ringed compounds accounted for 68% of the PAHs. Further, carcinogenic PAHs (BaA, Chry, BbF, BkF, BaP, DahP, Inp) possessed highest cancer risk (CR = 2.09 × 10−3) to the local population when exposed to the sediments from the studied area and ingestion was found to be the primary process of contamination. The study strongly recommends a systematic monitoring of POPs and PAHs, being the Hooghly River water used by local people for their livelihood. Highlights • High exposure through ingestion suggests higher risk due to biomagnification. • PAH sources were both from pyrolytic and petrogenic origins together. • PAH carcinogenic potential were lower than other Indian and Asian river estuaries. • p,pʹ -DDE and o,pʹ -DDT exceeded the average global concentration. • α-HCH/γ-HCH indicated sources from lindane and HCH technical mixtures. [ABSTRACT FROM AUTHOR]