The progress of space exploration towards establishing human colonies on extraterrestrial bodies, coupled with the pressing need to address the climate crisis on Earth, underscores the significance of developing sustainable and self-sufficient cultivation techniques. A review of the existing literature reveals that most research in this area has concentrated on the operation and control of robotic hydroponic systems, often applied to off-the-shelf designs. However, by focusing solely on operational aspects, past research may have overlooked opportunities for significant resource savings that could be achieved through structural optimization. We propose in this paper a framework to optimize the structure of an automated Nutrient Film Technique (NFT) hydroponic system to minimize resource consumption (e.g. energy and plant nutrients), mass and volume. The modelling and optimization process employs Multidisciplinary Design Analysis and Optimization (MDAO) techniques to accommodate the diverse range of disciplines involved and the multiple optimization objectives of the system. The proposed framework considers the composition of the crew and computes the optimal structure tailored to meet their dietary requirements, based on the selected optimization objectives. To evaluate the system’s performance, our framework incorporates criteria inspired by the innovative Advanced Life Support System Evaluator (ALiSSE), developed by the European Space Agency (ESA), which offers a comprehensive system approach for assessing life support systems. Through rigorous analysis, consistency of the model and optimization is demonstrated, yielding expected results, and affirming the effectiveness of the approach.