Subirrigation systems are widely used in commercial greenhouses for efficient and high-quality production of potted plants. However, proper criteria of the water level and retention time need to be quantified for more efficient irrigation. This study analyzed the water absorption and vertical water distribution in a horticultural substrate in 10-cm pots under various subirrigation water levels and retention times. To analyze the water absorption dynamics, we continuously measured changes in the actual substrate volumetric water content using capacitance soil moisture sensors. The vertical distribution of water in the pot was measured using a thermal imaging camera, with a small temperature difference indicating more water absorption. As expected, the volumetric water content in the pots increased as the subirrigation water level and retention time increased; however, significantly less water was absorbed near the top surface of the substrate, and the variation of the vertical water distribution increased at lower subirrigation water levels or shorter retention times. This suggests that young plants with smaller root systems would require a higher water level and retention time for subirrigation if their roots are distributed near the top of the pot. This study provides a better understanding of water absorption and its vertical distribution across a horticultural substrate when using a subirrigation system and supports decision making for the suitable management of subirrigation conditions according to the type of plant species or crop growth stage.