The sediment pollution caused by different metals has attracted a great deal of attention because of the toxicity, persistence, and bio-accumulation. This study focuses on heavy metals in the hyporheic sediment of the Weihe River, China. Contamination levels of metals were examined by using “geo-accumulation index, enrichment factor, and contamination factor” while ecological risk of metals were determined by “potential ecological risk and risk index”. The pollutant accumulation of metals ranked as follows: “manganese (Mn) > chromium (Cr) > zinc (Zn) > copper (Cu) > nickel (Ni) > arsenic (As) > lead (Pb)”. The geo-accumulation index identified arsenic as class 1 (uncontaminated to moderate contamination), whereas Cu, Cr, Ni, Zn, Pb, and Mn were classified as class 0 (uncontaminated). According to the enrichment factor, arsenic originated through anthropogenic activities and Cr, Ni, Cu, Zn, and Pb were mainly controlled by natural sources. The contamination factor elucidated that sediments were moderately polluted by (As, Cr, Cu, Zn, Mn, and Pb), whereas Ni slightly contaminated the sediments of the Weihe River. All metals posed a low ecological risk in the study area. The risk index revealed that contribution of arsenic (53.43 %) was higher than half of the total risk.