Particles in a substrate create a network of pore pathways for water to move through, with size and shape determining the efficacy of these channels. Reduced particle size diversity can lead to increased leachate, poor substrate hydration, and an inefficient irrigation practice. This research examined the hydration characteristics of three greenhouse substrate components at three preconditioned initial moisture contents using subirrigation under five different irrigation durations and three water depths (2 mm, 20 mm, and 35 mm). Sphagnum peatmoss, coconut coir, and aged pine bark were tested at 67%, 50%, and 33% initial moisture (by weight). The objectives were to determine the impact of varying irrigation event durations (5, 10, 20, 30, 60 min) over a 60-min period, and the further influence of water depth and initial moisture, on the water capture abilities of peat, coir, and pine bark. The number of irrigation events depended on the irrigation event time of that experimental unit divided by the total time of 60 min, varying from 12, 6, 3, 2, and 1 event. Hydration efficiency was influenced by initial moisture content (IMC), water depth, pulsing duration, and inherent substrate characteristics (hydrophobicity/hydrophilicity). Initial MC had the largest impact on peat, regardless of water level or irrigation duration. Lower IMCs increased the hydrophobic response of peat, further reducing the amount of water the substrate was able to absorb. Pine bark had a 5–10% decrease in initial hydration between 67%, 50%, and 33% IMC, while coir’s hydrophilic nature reduced any IMC affects. At 50% IMC or less, coir had the highest volumetric water content (VWC) across all substrates, pulsing durations, and water depths. Water depth was found to increase initial hydration and final hydration 6–8% across all substrates. These three materials had altered and varied water capture responses depending on the combination of treatments employed. This work demonstrated the effects of intensity and exposure on substrates and the need for more integrated research for improving water use efficiency on container crops.