Abstract: Aim The Kallada River is exposed to several kinds of pollution from domestic, civic, recreational, and agricultural activities and human settlements. The objectives of the study were to assess sediment quality, especially the trace metal concentration and to compare with the previous reports on the sources of pollutants in the Kallada River. Methods A total of 12 sediment variables including the following metals: iron (Fe), manganese (Mn), chromium (Cr), and zinc (Zn) were analyzed. Atomic Absorption Spectrophotometer (AAS) was used to detect trace metal concentration in the sediment samples. Statistical tools such as Pearson’s correlation, Principal component analysis (PCA), and Cluster analysis (CA) were employed to analyze the data and source of pollutants. Results This investigation indicated that Fe was the most accumulated element in the sediments, and the midstream (K6 and K10) and downstream sites (K11 to K15) showed a much higher concentration level than the upstream sites. The concentrations of trace metals in sediment samples followed the order Fe> Mn> Cu>Zn. Conclusions The present study concluded that major sources of pollutants were sewage and civic effluents and agricultural discharges. These may cause a severe threat to the Kallada River and health risk to the local populations, which rely on the river, primarily for drinking purposes. Hence, appropriate conservation policies to reduce pollution are therefore essential.