Effective water and soil management is crucial for crop productivity, particularly in rice cultivation, where poor soil quality and water scarcity pose challenges. The response of deeper-rooted rice grown in soils amended with different soil amendments (SAs) to Internet of Things (IoT)-managed alternate wetting and drying (AWD) irrigations remains undetermined. This study explores the effects of various SAs on DRO-1 IR64 rice plants under IoT-based soil moisture monitoring of AWD irrigation. A greenhouse experiment executed at the Tokyo University of Agriculture assessed two water management regimes—continuous flooding (CF) and AWD—alongside six types of SAs: vermicompost and peat moss (S + VC + PM), spirulina powder (S + SPP), gypsum (S + GS), rice husk biochar (S + RHB), zeolite (S + ZL), and soil without amendment (S + WA). Soil water content was continuously monitored at 10 cm depth using TEROS 10 probes, with data logged via a ZL6 device and managed through the ZENTRA Cloud application (METER GROUP Company). Under AWD conditions, VC + PM showed the greatest decline in volumetric water content due to enhanced root development and water uptake. In contrast, SPP and ZL maintained consistent water levels. Organic amendments like VC + PM improved soil properties and grain yield, while AWD with ZL and GS optimized water use. Strong associations exist between root traits, biomass, and grain yield. These findings highlight the benefits of integrating SAs for improved productivity in drought-prone rice systems.