Appropriate soil management practices and correct use of agrochemicals for crop protection are essential to alleviate stresses that affect the quality and yield of pecans [Carya illinoinensis (Wangenh.) K. Koch]. A greenhouse study was conducted to evaluate the effect of soil surface manipulation and indaziflam application on evapotranspiration (ET) and gas exchange parameters of pecan trees, and phytotoxicity effects of indaziflam on pecan trees. Trees were planted in large pots with a homogeneous porous media (HM), including the controls (C), preferential flow channels open at the soil surface (PF), and preferential flow channels with surface soil manually tilled to 5 cm depth [shallow tillage (ST)]. Trees with HM, PF, and ST were treated with 50 g a.i./ha of indaziflam in 2014 and 2015, whereas an application rate of 150 g a.i./ha was used for trees with HM and ST in 2016. All trees were irrigated about every 14 days with 7 L of water in 2014 and 2015, and 5 L in 2016. A water balance analysis determined the ET in different treatments in 2014 and 2015. Gas exchange parameters were measured before and after irrigation in 2015 and 2016. Photosynthetic rates in C, HM, PF, and ST were consistently significantly lower before than after irrigation. PF and ST did not decrease the available water content of the soil because there was no significant difference in the volume of effluent, ET, and gas exchange parameters among the treatments. No herbicide injury symptoms and no influence on gas exchange parameters and ET were observed after using both application rates of indaziflam.