We studied the importance of environmental drivers for the seasonal dynamics of gross primary production (GPP), ecosystem respiration (R), and net ecosystem production in surface waters of two tropical lakes in southeast Brazil (Carioca - CA; and Dom Helvécio - DH), 2011 and 2012, using high frequency measurements of dissolved oxygen. Metabolic rates were approximately twice as high during the fully mixed winter periods, compared to the summer periods. For both lakes, GPP was approximately 30% lower during the warmer and dryer spring of 2012 compared to 2011. Seasonal changes in GPP and R were negatively correlated to water column stability (GPP r = -0.82, p < 0.001; R r = -0.80, p < 0.001). Periods with high stability coincided with warm waters which reduced mixing and internal inputs of nutrients from hypolimnetic waters. GPP was accordingly suppressed in both lakes during summer due to a combination of nutrient depletion and photo-inhibition, which was more pronounced during summer. These conditions were more prevailing during the warm and dry year of 2012, indicating ecosystem responses in carbon cycling to the ongoing regional climate changes.