As growers face increasing constraints on water use, understanding disease risks associated with deficit irrigation is paramount. Previous studies with Phytopthora capsici root and crown rot in tomato indicate that DI increases latent infection and disease risks. This work evaluates how different substrates influence DI-associated disease risk in containerized annuals, with a focus on an annual vegetable (tomato) and floricultural crop (chrysanthemums). We hypothesized that substrates with greater water holding capacity (e.g., peat) would present a lower disease risk under DI due to less plant water stress. We evaluated three substrates: Bark, Fiber, and Peat; and two irrigation schemes: “Well-Watered” and “Deficit”. Phytopthora capsici alone increased root necrosis in all treatments (P < 0.001), as did P. capsici and Deficit together (P < 0.001). Comparing measurements among substrates, disease risk was lowest in Bark, intermediate in Peat and greatest in Fiber (P < 0.05). Similar results were observed in studies with Chrysanthemum and Phytopythium helicoides, suggesting that substrate may influence the risk of DI. More work is needed to elucidate the details of that relationship and translate to field soils.