Climate change is increasing the crop water requirement necessitating the need to increase crop water use efficiency. Soil moisture content can have a dramatic impact on water use efficiency and crop productivity by influencing photosynthesis and plant growth rates. Open hydroponics system (OHS) a method of supplying a crop’s nutrient and water needs continuously with intensive fertigation and irrigation has the potential to improve water use efficiency. We investigated the effect of soil moisture under an OHS on net photosynthetic and transpiration rates in young citrus. The experiment was conducted under field conditions from Sept 2009 to May 2010 in a randomized complete block design (RCBD) with three treatments and four replications. The treatments included microsprinkler irrigation with granular fertilizer application (conventional with infrequent irrigation), daily microsprinkler fertigation, and daily drip fertigation (OHS). The fertigation treatments were controlled with automatic programmable fertigation systems with remote controls. Soil moisture sensors (capacitance probes) were installed within (0-10 cm) and below (46 cm) the root zone in each treatment. Stomatal conductance, transpiration and photosynthesis were evaluated by measuring gas exchange using a portable photosynthesis system (LI-COR 6400). Our results showed that fertigation treatments had higher stomatal conductance (28%), transpiration (42%) and photosynthesis (30%). None of these physiological parameters were influenced by the changes in soil moisture content in fertigation treatments. However, photosynthetic rates in the conventional treatment were lowest and responded to the changes in soil moisture content which was often limiting in the root zone. Fertigation treatments had the higher plant growth (1.3-1.5x) and water use efficiency (2-3x) as compared to the conventional treatment. The results suggested that maintaining root zone water content near field capacity with frequent small irrigations can substantially minimize physiological stress, maximize gas exchange and photosynthesis, and improve plant growth.