Hypoxia is a well-recognized condition reducing biodiversity and increasing greenhouse gas emissions in aquatic ecosystems, especially under warmer temperatures of tropical waters. Anoxia is a natural event commonly intensified by human-induced organic inputs in inland waters. Here, we assessed the partial pressure of O₂ (<i>p</i>O₂) and CO₂ (<i>p</i>CO₂), and the ratio between them (represented by the respiration index, RI) in two oligotrophic lakes of the Atlantic Tropical Forest, encompassing dry and rainy seasons over 19 months. We formulated the hypothesis that thermal stratification events could be coupled to natural hypoxia in deep waters of both lakes. Our results indicated a persistence of CO₂ emissions from these tropical lakes to the atmosphere, on average &plusmn; standard error (SE) of 17.4 mg C m⁻² h⁻¹ probably subsided by terrestrial C inputs from the forest. Additionally, the thermal stratification during the end of the dry season and the rainy summer was coupled to anoxic events and very low RI in deep waters, and to significantly higher <i>p</i>O₂ and RI at the surface (about 20 000 μatm and 1.0, respectively). In contrast, the water mixing during dry seasons at the beginning of the winter was related to a strong destratification in <i>p</i>O₂, <i>p</i>CO₂ and RI in surface and deep waters, without reaching any anoxic conditions throughout the water column. These findings confirm our hypothesis, suggesting that lakes of the Atlantic Tropical Forest could be dynamic, but especially sensitive to organic inputs. Natural anoxic events indicate that tropical oligotrophic lakes might be highly influenced by human land uses, which increase organic discharges into the watershed.