The present study had as its main objective the evaluation of the heat balance method in young orange and mango plants under protected environment. The work was carried out at Embrapa Cassava and Tropical Fruits, Cruz das Almas, BA. Later on, estimates of sap flow were conducted for two mango plants cultivated in pots of 15 and 50 L installed on weighting platforms of 45 and 140 kg; sap flow was determined in three orange plants, two of which were also installed on weighing platforms. The values of sap flow were compared to the transpiration measured by lysimeters at integrated intervals of 1, 2, 4 and 24 h. The heat balance method showed good precision for estimating daily transpiration (R² = 0.95 and R² = 0.90), accompaning the availability of energy in the system, underestimating on average 4.6% of the daily transpiration in orange plants and overestimating in about 0.3% the daily transpiration of mango plants under conditions of good water supply. The heat balance method underestimated by 16% the transpiration in orange under conditions of water deficit.