Urban contamination resulting from the dynamics of unplanned cities has generated interest in recent decades due to increased pollutant emissions into the natural environment. The Coata River is a complex ecosystem exposed to pollution due to the high urbanization degree and consequent industrial dynamics, as well mining activities. Significant amounts of waste and pollutant substances are discharged into the river, often without any treatment, contributing to a drastic increase in the concentration of heavy metals that cause impacts and pressures on the environment. In this context, the present study contributes to the evaluation of the metal concentration (Zn, Cu, and Co) in three short sediment cores sampled at Coata River, Puno region, Peru. The acquired concentration data was compared with guideline reference values established by international sediment quality standards and used for calculations of the geochemical indices Enrichment Factor and Geoaccumulation Index. The highest concentrations were found for zinc (639 mg/kg) and copper (96 mg/kg), whilst zinc exhibited some values above the guidelines corresponding to the probable effect level (PEL, legislation of Canada) and mean range effects (ER-M, legislation of the United States). According to the sediment quality indices, the three stations range from moderately to highly contaminated with Zn, while Cu and Co show no contamination and moderate contamination, originating from both geogenic and anthropogenic sources.