Short rotation woody crops (SRWC) are bred for rapid growth properties. Knowledge of how varying environmental conditions and endophytic bacteria impact physiology are needed to make planting recommendations. Three eastern cottonwood (EC) and three hybrid poplar (HP) varietals were planted in replicate blocks at upland and alluvial sites. Whole-tree water use and water use efficiency (WUE) were measured using heat-dissipation sap flow and related to overall productivity. Productivity measurements were higher at the upland site. Sap flow was higher at the upland site and for endophyte treated individuals. WUE was higher at the alluvial site and for EC. WUE and leaf area index (LAI) were significantly correlated with biomass (negatively and positively respectively). Overall, HP performed better at the upland site, EC at the alluvial site. These results are beneficial in further testing of optimal site and genotype pairings for SRWC.