This study aimed at evaluating the occurrence of stratification/equalization cycles in two full-scale shallow maturation ponds in Brazil, with different operational configurations and different periods of the year, through monitoring of temperature and other constituents in the vertical profile of the ponds. The study comprised two operational phases: one phase in which both ponds had no baffles and operated in parallel (one pond had sludge accumulated on the bottom while the other did not); and another phase in which the ponds operated in series, the first pond without baffles and with accumulated sludge on the bottom while the second pond had two longitudinal baffles, a shallower depth and no accumulated sludge. Overall, there were systematic daily periodic events of thermal stratification followed by temperature equalization and vertical mixing in both ponds and operating phases. Vertical temperature gradients were predominantly in the 0–7 °C m−1 range. Statistical tests showed a significant positive correlation between the thermal gradient in the pond and air temperature, but not between the thermal gradient and wind speed. Data suggested that ponds remained 56% of the time under thermal stratification and 44% in vertical mixing. The data also highlighted the importance of sludge in the thermal balance of ponds.