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Anthropogenic climate change—combined with increased human-caused ignitions—is leading to increased wildfire frequency, carbon dioxide emissions, and refractory black carbon (rBC) aerosol emissions. This is particularly evident in the Amazon rainforest, where fire activity has been complicated by the synchronicity of natural and anthropogenic drivers of ecological change, coupled with spatial and temporal heterogeneity in past and present land use. One approach to elucidating these factors is through long-term regional fire histories. Using a novel method for rBC determinations, we measured an approximately 3500-year sediment core record from Lake Caranã in the eastern Amazon for rBC influx, a proxy of biomass burning and fossil fuel combustion. Through comparisons with previously published records from Lake Caranã and regional evidence, we distinguished between local and regional rBC emission sources demonstrating increased local emissions of rBC from ~1250 to 500 calendar years before present (cal yr BP), coinciding with increased local-scale fire management during the apex of pre-Columbian activity. This was followed by a regional decline in biomass burning coincident with European contact, pre-Columbian population decline, and regional fire suppression associated with the rubber boom (1850–1910 CE), supporting the minimal influence of climate on regional burning at this time. During the past century, rBC influx has rapidly increased. Our results can serve to validate rBC modeling results, aiding with future predictions of rBC emissions and associated impacts to the climate system.