Acute shortage of water resources and high unproductive water losses are the key problems of irrigated agriculture in arid regions. One of the possible solutions is to optimize soil water retention using natural and synthetic polymer water absorbers. Our approach uses the HYDRUS-1D design to optimize the placement of organic water absorbents such as peat and composite hydrogels in the soil profile in the form of water-storing capillary barriers. Field testing of the approach used a water balance greenhouse experiment with the cultivation of butternut squash (butternut squash (Cucurbita moschata (Duchesne, 1786)) under sprinkler irrigation with measurement of the soil moisture profile and unproductive water losses in the form of lysimetric water outflow. In addition, the biodegradation rate of organic water absorbents was studied at the soil surface and at a depth of 20 cm. Organic capillary barriers reduced unproductive water losses by 40–70%, retaining water in the topsoil and increasing evapotranspiration by 70–130% with a corresponding increase in plant biomass and fruit yield. The deepening of organic soil modifiers to the calculated depth not only allowed capillary barriers to form, but also prevented their biodegradation. The best results in soil water retention, plant growth and yield according to the “dose-effect” criterion were obtained for a composite superabsorbent with peat filling of an acrylic polymer matrix. The study showed good compliance between the HYDRUS design and the actual efficiency of capillary barriers as an innovative technology for irrigated agriculture using natural and synthetic water absorbents.