Alluvial gold mining activities in the Peruvian Amazon rainforest are responsible for mercury emissions and deforestation. To understand related environmental impacts, specifically toxicity and climate change, this study uses Life Cycle Assessment methodology. Four predominant extraction systems were selected and modelled and three scenarios that reflect currently available gold recovery systems were modelled: amalgamation, amalgamation with mercury recovery through retort system and gravimetric tables. The USEtox and IPCC life cycle impact assessment methods were used to assess the environmental impacts in term of human toxicity, freshwater ecotoxicity and climate change. Results show that for all systems, human toxicity values are governed by mercury emissions in gold recovery activities (ca. 80%). However, the use of retort significantly lowers these impacts (ca. 90%). Machines and diesel use for ore extraction and freighting activities drive freshwater ecotoxicity. Moreover, deforestation has a major contribution on the environmental impacts related to climate change. However, these impacts are dependent on the type of extraction system. Although human toxicity, freshwater ecotoxicity and climate change are frequently studied separately, a direct relationship between them has been identified in this system. Finally, beyond the environmental burdens related to alluvial gold mining, there are impacts affecting the social, cultural, and economic dimensions that will need to be analyzed to ensure a comprehensive understanding of the system.