The main objectives of this research were to determine the response of inorganic and organic soil conditioners to phenotypic traits of rice and soil physicochemical properties of soil under water deficit. The experiments were designed in a 2 × 2 factorial with duplicates for 20 weeks in the greenhouse. The treatments consisted of different types of soil ameliorants and a hybrid mixture of substrates which were natural zeolite, GFOC, hybrid (natural zeolite + GFOC), and control. All treatments received 60% water capacity, while control received 100% water after 30 days of sowing (DAS). The soil physicochemical properties were observed along with phenotypic traits of rice such as plant height. The study found that there were slight changes in pH value before and after those treatments, ranging between 4.7 and 5.4 with optimum pH of 4.9 in hybrid treatment. Hybrid treatment soil exhibits a significant increase in moisture content between 5.286 and 7.623%, while control treatment exhibits a decrease in moisture content from 6.835 to 4.934%. When compared to all treatments at 14 DAS (vegetative stage), plants treated with hybrid soil conditioners displayed the highest plant height of 18.3 cm, followed by GFOC (17.8 cm), natural zeolite (16.3 cm), and control (14.6 cm). However, at 28 DAS hybrid and GFOC treatments started to wither and completely died after 49 DAS compared to control and natural zeolite treatments. Nonetheless, there was a fluctuation pattern of plant height for control treatment compared to natural zeolite showing no changes after being put under water stress at 30 DAS. It was found that the soil conditioner helps the plants survive in unfavorable soil conditions with proper nurture to improve rice growth performance.