Growers rely on soilless substrates to provide sufficient water and nutrients to containerized crops. Traditional bark-based substrates are engineered to have relatively low water-holding capabilities, which can lead to nonuniform rewetting patterns and inefficient usage of water resources. Engineering substrates to redistribute water dynamics and maximize aeration within the container may improve water resource efficiencies. The goal of this study was to evaluate whether more efficient irrigation schedules can be used when stratifying unique substrates within a container for added crop water and nutrient efficiency. Loropetalum chinense ‘Ruby’ liners were planted and grown in a conventional pine bark substrate or one of three stratified substrate treatments, including a bark:peat, bark:coir, or fine bark layered on top of a coarse bark. The crops were grown under four different irrigation schedules, including single daily application, single application at deficit levels, cyclic application, or cyclic at deficit schedules. Stratified substrates improved crop growth, quality, and yield when compared with plants grown in conventional bark in the single application irrigation treatment. Measured at final harvest, substrates positively influenced plant growth index (P < 0.0001), whereas irrigation scheduling alone had no effect (P = 0.6321). There was a strong interaction between substrate and irrigation schedules on Δ growth index (P = 0.0141). There were strong substrate effects on shoot dry weight (P = 0.0060), root dry weight (P = 0.0342), and growth index (P = 0.0040). The stratified bark:coir treatment outgrew all other substrate treatments. In addition, within all irrigation treatments, plants grown with the stratified bark:coir substrate had the highest survival ratings among the other substrate treatments, whereas the conventional bark had the lowest survival rates. Substrate and irrigation had an effect on nitrogen and potassium leachate concentrations levels (P = 0.0107 and P = 0.0004, respectively). Evaluation of microbial communities showed that substrate (P = 0.0010) and the stratified layer (P = 0.0010) had strong influences on the type of community present and the relative abundance in the treatments used herein this study. Specifically, within cyclic scheduling, bark:peat actinomycete populations were significantly greater than other substrate treatments. Furthermore, under deficit irrigation, stratified substrate systems were able to mitigate crop water stress. The results indicate that when crops such as the Loropetalum are grown in the stratified system, crop growth can be sustained when drought conditions are present. This is possible by providing adequate water availability even under low water inputs until subsequent irrigations during the fragile establishment period, when compared with using traditional bark-based substrates.