This study explores the extent and possible sources of heavy metal (Cd, Cr, Cu, Fe, Mn, Pb, Zn and Ni) contamination in the bed sediments of the Gomti River performing principal component analysis on the five years (Jan. 1994–Dec. 1998) data set obtained through continuous monitoring of the river water and bed sediments at eight selected sites and water/wastewater of its tributaries/drains. Influence of anthropogenic activities on metal contamination of the bed sediments was evaluated through computing the geoaccumulation index for various metals at studied sites. PCA performed on combined (river bed sediment, water, suspended solids, water/wastewater from tributaries/drains) data set extracted two significant factors explaining more than 58% of total variance. Factor loadings suggested the presence of both natural as well as anthropogenic sources for all these metals in the river bed sediments. Among all the sites, the sites 4 and 5 are more contaminated with Cd, Cu, Cr and Pb, which was supported by the geoaccumulation indices computed for metals. Factor scores revealed presence of seasonal (monsoon-related) differences in metals profiles for river water and suspended solids and absence of seasonal differences for bed sediment and wastewater. Further, the metal contamination of the bed sediment was also evaluated using biological thresholds. Results suggested that the river bed sediments are contaminated with heavy metals, which may contribute to sediment toxicity to the freshwater ecosystem of the Gomti River.