River sediments act as sinks and indicators of anthropogenic influences, reflecting contamination from both watershed and atmospheric inputs. The downstream reaches of the Periyar River, one of the most industrialized stretches in Kerala, are increasingly threatened by untreated industrial effluents and sewage discharges, posing risks to aquatic ecosystems and public health. To assess ecological security, surface sediment samples from 21 locations were analyzed for grain size, total organic carbon (TOC), and seven heavy metals (V, Cr, Co, Ni, Cu, Zn, Pb). Pollution status was assessed using descriptive statistics, the geo-accumulation index (Igeo), pollution load index (PLI), contamination indices (CF, mCd, Cd, Cp), and potential ecological risk index (RI). Multivariate statistical tools, including Pearson’s correlation, principal component analysis (PCA), and cluster analysis, were employed to identify pollution sources. The average heavy metal concentrations followed the order: Zn (422.43) > Cr (168.10) > V (151.10) > Ni (96.76) > Cu (79.38) > Pb (26.29) > Co (22.10) mg/kg. The PLI indicated moderate pollution, mainly driven by V, Cr, Cu, and Zn. The RI suggested a considerable ecological risk from Ni, and moderate risks from Pb and Cu. Source apportionment revealed that V, Cr, Zn, and Pb originated primarily from domestic, traffic, agricultural, and petrochemical sources, Co and Ni from mixed natural and industrial sources, and Cu from traffic and industrial activities. Overall, the results highlight that industrial and domestic inputs are the dominant contributors of heavy metals in the study area. These findings provide a strong scientific basis for implementing stricter monitoring and effluent pretreatment strategies to protect sediment quality and safeguard the riverine ecosystem.