We tested an approach to estimate daily canopy net photosynthesis, A, based on estimates of transpiration, E, using measurements of sap flow and water-use efficiency, omega, by measuring delta 13C in CO2 respired from shoots in the canopies of two conifers (Podocarpaceae) native to New Zealand. The trees were planted in adjacent 20-year-old stands with the same soil and environmental conditions. Leaf area index was lower for Dacrycarpus dacrydioides D.Don in Lamb (1.34 m2 m-2) than for Podocarpus totara G.Benn. ex D.Don var. totara (2.01 m2 m-2), but mean (+/- standard error) stem diameters were the same at 152 +/- 21 mm for D. dacrydioides and 154 +/- 25 mm for P. totara. Over a 28-day period, daily A (per unit ground area) ranged almost five-fold but there were no significant differences between species (mean 2.73 +/- 1.02 gC m-2 day-1). This was attributable to higher daily values of E (2.63 +/- 0.83 mm day-1) and lower omega (1.35 +/- 0.53 gC kg H2O-1) for D. dacrydioides compared with lower E (1.82 +/- 0.72 mm day-1) and higher omega (1.90 +/- 0.77 gC kg H2O-1) for P. totara. We attributed this to higher nitrogen availability and nitrogen concentration per unit foliage area, Na, and greater exposure to irradiance in the D. dacrydioides canopy compared with P. totara. Our findings support earlier observations that D. dacrydioides is more adapted to sites with poor drainage. In contrast, the high retention of leaf area and maintaining low rates of transpiration by P. totara, resulting in higher water-use efficiency, is an adaptive response to survival in dry conditions. Our findings show that physiological adjustments for two species adapted to different environments led to similar canopy photosynthesis rates when the trees were grown in the same conditions. We demonstrated consistency between whole-tree and more intensive shoot-scale measurements, confirming that integrated approaches are appropriate for comparative estimates of carbon uptake in stands with different species.