This paper presents a first integrated survey on the occurrence and distribution of geogenic contaminants in groundwater resources of Western Amazonia in Peru. An increasing number of groundwater wells have been constructed for drinking water purposes in the last decades; however, the chemical quality of the groundwater resources in the Amazon region is poorly studied. We collected groundwater from the regions of Iquitos and Pucallpa to analyze the hydrochemical characteristics, including trace elements. The source aquifer of each well was determined by interpretation of the available geological information, which identified four different aquifer types with distinct hydrochemical properties. The majority of the wells in two of the aquifer types tap groundwater enriched in aluminum, arsenic, or manganese at levels harmful to human health. Holocene alluvial aquifers along the main Amazon tributaries with anoxic, near pH-neutral groundwater contained high concentrations of arsenic (up to 700 μg/L) and manganese (up to 4 mg/L). Around Iquitos, the acidic groundwater (4.2 ≤ pH ≤ 5.5) from unconfined aquifers composed of pure sand had dissolved aluminum concentrations of up to 3.3 mg/L. Groundwater from older or deeper aquifers generally was of good chemical quality. The high concentrations of toxic elements highlight the urgent need to assess the groundwater quality throughout Western Amazonia.