Legislation governing strict-protection nature reserves in Brazil in principle precludes human habitation, but virtually all Amazon reserves are nonetheless inhabited. Historical ecology research reported herein assesses the impacts of occupation and resource use by beiradeiros (forest peasants) on the forests of a strictly designated nature reserve in the Iriri River basin (Brazilian Amazon). The hypothesis is that traditional beiradeiros activities are congruent with the aims of conservation of the reserve because their impacts are either neutral or enhance diversity of forest landscapes and biota. We designed the methodology underlying data collection to integrate forest inventory with archaeological techniques in two contrasting forest types (terra firme and seasonally inundated forest), faunal surveys, freelisting of tree terms by beiradeiros, and participant observation, in order to determine biological diversity indices, forest age and the parameters of traditional knowledge that encode such diversity in local vocabulary. Our research results lead us to reject the premise that traditional peasant activities lead to ecological degradation or impoverishment, and suggest that the rationale underpinning strictly protected nature reserves should be re-examined.