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Climate warming is increasing thermal stratification depth, strength, and duration in lakes, leading to more frequent hypolimnetic oxygen depletion. Most research has focused on eutrophic temperate lakes, which differ significantly from boreal lakes that dominate Earth’s landscape. However, assessing the impact of hypoxia, confounded by browning, warming, and altered stratification, on biogeochemistry and ecological processes in boreal lakes is particularly challenging. Here, we test how oxygenating a hypoxic hypolimnion affects water chemistry, bacterial and primary production (BP and PP), and detritus degradation in a shallow humic boreal lake divided into two basins in an experimental four-year Before-After Control-Impact (BACI) design. After two control years, we oxygenated the hypolimnion of one basin during two stratified periods without disturbing the seasonal development of the thermocline. Hypolimnetic oxygen concentrations moderately impacted lake biogeochemistry. Reoxygenation altered nitrification pathways (increased NO3−) of the hypolimnion, and slightly decreased epilimnion and lake BP (− 6.1% of annual average) and green tea degradation (− 6.0%), whereas Rooibos degradation slightly increased (7.3%). Other water chemistry parameters remained within natural variation. We compared our BACI approach, which separates natural variation, to the simpler Before vs After approach, which does not. We find that studies not accounting for seasonal and among-year variability may overestimate the effects of oxygenation on hypolimnion biogeochemistry, as much of the observed impact is due to natural climate variation. Climate warming and altered stratification patterns are therefore likely to impact boreal lake algal and bacterial production and degradation more than hypolimnion hypoxia during the stratified period.