The present study includes a systematic analysis of sediment contamination by heavy metals of the River Ghaghara flowing through the Uttar Pradesh and Bihar in Indian Territory. To estimate the geochemical environment of the river, seven heavy metals, namely Co, Cu, Cr, Ni, Cd, Zn, and Pb were examined from the freshly deposited river bed sediment. All the sediment samples were collected on a seasonal basis for the assessment of fluctuation in 2014-2015 and after preparation samples were analyzed using standard procedure. Result showed that heavy metal concentration ranged between 11.37 and 18.42 mg/kg for Co, 2.76 and 11.74 mg/kg for Cu, 61.25 and 87.68 mg/kg for Cr, 15.29 and 25.59 mg/kg for Ni, 0.21 and 0.28 mg/kg for Cd, 13.26 and 17.59 mg/kg for Zn, 10.71 and 14.26 mg/ kg for Pb in different season. Metal contamination factor indicates the anthropogenic input in the river sediment was in the range of (0.62-0.97) for Co, (0.04-0.26) for Cu, (0.68-0.97) for Cr, (0.22-0.38) for Ni, (0.70-0.93) for Cd, (0.14-0.19) for Zn, and (0.54-0.71) for Pb. The highest contamination degree of the sediment was noticed as 4.01 at Ayodhya and lowest as 3.16 at Katerniaghat. Geo-accumulation index was noted between (0 and 1) which showed that sediment was uncontaminated to moderately contaminated and may have adverse affects on freshwater ecology of the river. Pollution load index (PLI) was found highest at Chhapra which was 0.45 and lowest at Katerniaghat which was 0.35 and it indicates that the river sediment has a low level of contamination. Significant high correlation was observed between Co, Cu, and Zn, it suggests same source of contamination input is mainly due to human settlement and agriculture activity. Positive correlation between Zn, Co, Cu, Cr, and Ni indicated a natural origin of these elements in the river sediment. Cluster analysis suggests grouping of similar polluted sites. The strong similarity between Co, Zn, Pb, Ni, Cu, and Cd showed relationship of these metals come from the same origin, which is possibly from natural and anthropogenic input which was also confirmed by correlation analysis. Using the various pollution indicators it was found that the river bed sediment is less contaminated by toxic metals during the study but the sediment quality may degrade in the near future due to increasing anthropogenic inputs in the river basin, hence proper management strategies are required to control the direct dumping of wastewater in the river.