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Most citrus nurseries in Florida, USA use overhead irrigation, but subirrigation methods, including ebb-and-flow and capillary mats, have been shown to conserve water and accelerate plant growth relative to overhead irrigation for other nursery species and may be a viable alternative to overhead irrigation in citrus liner production. The objectives of this study were to (1) automate an ebb-and-flow system for citrus liner production using capacitance sensors, and (2) evaluate how subirrigation and overhead irrigation methods affect water use, plant growth parameters, and substrate chemical properties. A study was conducted from 22 May to 23 September 2018 in which liners of six commercially important rootstock cultivars in cone-shaped containers were subjected to one of the following irrigation methods: ebb-and-flow triggered at substrate volumetric water contents (θ) of 0.24, 0.36, or 0.48 m3 m−3, capillary mats, and overhead irrigation. Capacitance sensors successfully monitored irrigation throughout the study. Ebb-and-flow benches used substantially less water (~411 L) than either capillary mats (13,098 L) or overhead irrigation (3193 L). By the end of the study, rootstock cultivars propagated using subirrigation methods were approximately 22% taller with 7% more total biomass than plants subjected to overhead irrigation. Additionally, plant growth at the 0.24 m3 m−3 threshold used to trigger ebb-and-flow was as great or greater than growth at 0.36 and 0.48 m3 m−3 thresholds. During the final five weeks of the study, substrate electrical conductivity was higher using subirrigation methods (0.84–1.3 ds m−1) than under overhead irrigation (0.55–0.8 ds m−1), but there were no symptoms of salt stress observed in plants at any time. Results from this study show that ebb-and-flow is a viable alternative to overhead irrigation and is superior to capillary mats for water conservation. In automated ebb-and-flow systems in Florida, we recommend using the 0.24 m3 m−3 threshold to produce the citrus rootstock cultivars used in this study with peat: perlite substrate. • Ebb-and-flow subirrigation was successfully automated for citrus liner production. • Ebb-and-flow benches used less water than capillary mats and overhead irrigation. • Liners under overhead irrigation generally grew slower than under subirrigation. • Triggering irrigation at 0.24 m3 m−3 substrate threshold optimized liner growth. • Ebb-and-flow is a viable alternative to overhead irrigation for liner production. [ABSTRACT FROM AUTHOR]