Abstract The natural radiation level has been determined for the sediment samples of the Ponnaiyar River with an aim of evaluating the radiation hazard. The mineralogical characterizations of the sediments have been carried out using the Fourier Transform Infrared (FTIR) spectroscopic technique. The relative distribution of major minerals is determined by calculating extinction coefficient. The concentration and spatial distribution of heavy metals (Pb, Cr, Cu, Zn and Ni) have been studied to understand the heavy metal contamination and its level of toxicity. To evaluate the potential toxicity, heavy metal concentrations are compared with different toxicological and geological reference values. The comparison results suggest that the present metals create an adverse effect on the aquatic ecosystems associated with this river. To assess the sediment contamination due to the studied heavy metals, the Pollution Load Index (PLI) is calculated. Multivariate Statistical analyses (Pearson Correlation, Cluster and Factor analysis) were carried out between the parameters obtained from radioactivity, mineralogical and geochemical analysis to know the existing relations. Obtained results showed that the effect of mineralogy on level of radioactivity should be significant. However, mineralogy effect on heavy metal composition in the sediments should be limited, indicating that other factors such as vicinity of the pollution sources are more important. Also, the influence of mineralogical characterization on level of radioactivity is significant, whereas the influence of the heavy metal composition on level of radioactivity should be limited.