Extensive areas of Amazonia undergo selective logging, modifying forest structure and nutrient cycles. Anthropogenic-accelerated rates of nitrogen (N) turnover could increase N loss and affect regeneration, carbon sequestration and timber production. We quantified leaf area reduction, canopy opening and downed biomass and resultant N flux from reduced impact logging (RIL) activities. We compared canopy reduction, surface soil moisture and nitrate to 8 m depth between logged gaps and intact primary forest to determine if logging activities increase subsoil nitrate. To test long-term logging effects, we evaluated surface N stocks along a 12-year postlogging chronosequence. At the harvest rate of 2.6 trees ha−1, total N additions in logging gaps, including leaves and wood from felled crowns (24.8 kg N ha−1) and other killed trees (41.9 kg N ha−1), accounted for over 80% of the total N addition to aboveground necromass from all logging activities (81.9 kg N ha−1). Despite this N turnover by logging, belowground nitrate storage to 8 m depth did not differ between logging gaps and primary forest at the low harvest rate and disturbance intensity of this study. Soil water depletion also did not differ between gaps and primary forest over 1 year, indicating the impact on belowground inorganic N was low. Compared with primary forest, nitrate concentrations to 8 m depth in logging gaps were only significantly higher at 60–100 cm, suggesting some N redistribution beyond the bulk of the fine roots in logging gaps. Extrapolated to the Amazon Basin scale, we provide a conservative estimate that logging damage and bole export under RIL would turn over 0.14 ± 0.07 to 0.23 ± 0.12 Tg N yr−1 based on 1999–2002 selective logging rates. Greater damage during conventional selective logging would cause higher N turnover throughout the Amazon Basin than our results based on RIL.