| Summary: | The increasing soil salinity levels under reclaimed water irrigation have a negative effect on plant growth. Greenhouse experiments were conducted in 2018 and 2019 under reclaimed water–fresh water combined irrigation. After transplanting (Day 1), rice was irrigated with clean water (tap water) for 10 days to facilitate rice root colonisation. Subsequently, rice was irrigated with reclaimed water for 50 days (Day 11 to 60), and then irrigated with clean water. <i>B. subtilis</i> and <i>S. cerevisiae</i> were mixed with clean water (tap water) and irrigated into soil at Day 61. <i>B. subtilis</i> (20 billion colony-forming units/g) and <i>S. cerevisiae</i> (20 billion colony-forming units/g) were mixed at the following proportions: 5 g and 0 (J1), 3.75 g and 1.25 g (J2), 2.5 g and 2.5 g (J3), 1.25 g and 3.75 g (J4), and 0 and 5 g (J5), respectively; rice treated with reclaimed water (CK) and clean water (J0) with no microorganisms applied were also used. We measured NO<sub>3</sub><sup>-</sup>-N and NH<sub>4</sub><sup>+</sup>-N concentrations and electrical conductivity (EC) in the soil at 0–5, 5–15, and 15–25 cm layers; root activity; and malondialdehyde (MDA), soluble sugar, superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and glutamine synthetase (GS) activity in leaves at Day 71. <i>B. subtilis</i> and <i>S. cerevisiae</i> combination could promote rice physiological indices, and <i>B. subtilis</i> had a greater effect than <i>S. cerevisiae</i>. There are obvious differences in the physiological performance and soil N between 2018 and 2019 due to the EC of reclaimed water. Redundancy analysis revealed that soil NO<sub>3</sub><sup>−</sup>-N and the mass of <i>B. subtilis</i> applied were major factors influencing leaf physiological indices. Five grams of <i>B. subtilis</i> is recommended to facilitate rice growth after irrigation with reclaimed water. Our research provides a new agronomic measure for the safe utilisation of reclaimed water.
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