The compensation heat pulse velocity (CHPV) is one of the most widely used methods to measure sap flow in woody plants. However, the accuracy of this method has not been fully explored especially for indigenous tree species of South Africa. The aim of this study was to evaluate the accuracy of the CHPV method in quantifying tree transpiration for selected tree species. Three indigenous trees sampled in a monolith form; black karee (Sersia lancea), buffalo thorn (Ziziphus mucronata) and wild olive (Olea africana) grown on weighing lysimeters (1 m × 1 m × 1.3 m) were installed with CHPV probes to measure sap flow on the stem half hourly, simultaneously with lysimeter measurements of transpiration. The surfaces of the lysimeters were covered with a 10 cm layer of Styrofoam, overlain by a 2 cm layer of gravel to minimize evaporation to a negligible level. Both the lysimeter and CHPV measurements were divided into two sets. The first set was used to develop tree specific calibration equations as well as an equation combining the three species used, here called a combination equation. The second set of data was used for validating the equations. Transpiration rates ranged from negligible at night to daily peaks of 3.5, 1.7 and 1.4 L h−1 for buffalo thorn, black karee and wild olive, respectively. Good agreement indices between CHPV and lysimeters were obtained when using both the tree specific equations and combination equation across species (D = 0.778–1.000, RMSE = 0.001–0.017 L h−1, MAE < 0.001 L h−1 and MBE = −0.0007 to 0.0008 L h−1). It was concluded that the CHPV method can accurately measure tree water use, and therefore can be useful for water resources management in forested areas.