In response to increasing pressure on arable land and freshwater resources, this study presents the conceptualisation and development of an integrated fertigation system tailored for the indoor cultivation of paddy (Oryza sativa). The system combines precision irrigation with nutrient delivery in a controlled environment, using sensor-based automation to monitor and regulate key parameters, including soil moisture content, electrical conductivity, and pH in real time. A modified hydroponic design was implemented to replicate paddy’s semi-aquatic conditions while avoiding traditional water-intensive flooding methods. The fertigation process is managed by a programmable logic controller (PLC), with control logic and feedback loops designed and simulated using MATLAB Simulink to optimise irrigation timing and nutrient dosing strategies. Additionally, a computational fluid dynamics (CFD) model was developed to analyse flow distribution and nutrient dispersion within the root zone, ensuring uniform delivery and mitigating risks of nutrient stratification or stagnation. Experimental trials conducted under LED-regulated photoperiods demonstrated a reduction in water usage by approximately 30% while maintaining effective nutrient uptake and consistent growth throughout the crop cycle. The system’s modular architecture allows scalability and adaptation to various spatial and climatic constraints. These findings highlight the potential of integrating CFD-based fluid analysis and simulation-driven control design with controlled-environment agriculture to promote sustainable, high-efficiency rice production in urban and climate-challenged settings.