Before environmental legislation was enforced, worldwide historical mines abandoned their operations without properly remediation and closure affecting the ecosystems. Because of its geological richness, Peru has attracted mining activities since colonial times and more than 8571 mining liabilities have been left. Pacococha and Millotingo mining liabilities are located on the banks of Aruri River, above Parac micro-watershed, from where communities of San Jose de Parac and San Antonio (San Mateo Huanchor district, Lima) take water for irrigating crops in low-flow periods. This paper reports for the first time in Peru the use of an interdisciplinary approach to examine the environmental effects of mining liabilities and small-scale mining on peasant communities. Physical and chemical methods, such as microscopy and spectrometry, were used to verify the presence of sulfides and to measure critical water quality parameters of Aruri and Rimac rivers. The ecosystem approach was applied to collect socioeconomic information from both communities; social actors and their statements regarding tailing problems were identified by social multi-criteria evaluation. It was found that the tailings contained sulfides that provide arsenic, cadmium, copper, zinc and manganese to Aruri and Rimac rivers in levels that exceed State of Oregon (USA) standard limits. It was also observed that both communities use this water to irrigate potato and alfalfa crops, well-known bioaccumulators. The tailings were classified as high risk to the environment by the Peruvian General Direction of Mining; however, future remediation remains uncertain due to a judicial dispute.