Subirrigation of containerized vegetable crops is a promising strategy to increase water and nutrient use efficiency, however, the longer growing seasons for cultivation of vegetable species may cause marked changes in the physical and chemical substrate properties. This study determined the effects of the irrigation system, subirrigation vs. drip-irrigation, and the concentration of the nutrient solution on the substrate physical and chemical properties in containerized tomato plants. Plants were irrigated with solutions at concentrations of −0.072, −0.058 and −0.043 MPa. Root dry weight of subirrigated plants was decreased by 35% in the substrate top layer when the highest concentration was used. Substrate electrical conductivity increased while pH was acidified as solution concentration increased and from the bottom to the top substrate layers in subirrigated plants. Salts buildup was associated with increased concentration of oxalic and tartaric acids and pH acidification. The improved substrate physical and chemical properties in subirrigated plants were associated with higher fruit yield (11.0 kg per plant) provided nutrient solution concentration was reduced to −0.043 MPa; in contrast, the highest yield in drip-irrigated plants (10.1 kg per plant) was obtained when the solution concentration was −0.072 MPa. In conclusion, subirrigation with reuse of the nutrient solution is a promising strategy to reduce water waste through runoff and leaching as water use efficiency increases due to greater water retention properties in the substrate, the maintenance of an EC within a range the plants can tolerate, and a lower acidification of substrate pH.2 of 13 60% [1]. In a previous paper, we are reporting that 1 L of water was required to produce 300 to 460 g of fruit, compared to 50 g in drip-irrigated plants, demonstrating that subirrigation increases water use efficiency by 6× to 9× [1].The movement of nutrients and water within growing media, and the subsequent chemical and physical properties, is dependent on the type of irrigation system used [2][3][4][5]. In surface irrigation, gravitational forces move water and nutrients downwards from the top of the container [6], affecting air and water retention capacities [2] and resulting in salt buildup in the lower portion of the growing media profile [6]. In contrast, subirrigation systems are based on the upward movement of water (capillary action) from the lower portion of the growing medium profile to the top of the container [6,7], thereby allowing a more uniform distribution of the nutrient solution throughout the substrate profile. The capillary movement of the nutrient solution in subirrigated containerized-plants reduces compaction of the growing media when compared to surface irrigation systems [8][9][10]. However, subirrigation causes a stratification of salts, which accumulate predominantly in the upper portion of the medium profile/layer [3,4]. Salt buildup in the upper layer of the medium negatively affects root and shoot growth, quality, and yield, espe...