Addressing the global demand for fresh water in communities and industries is a pressing concern. Over the years, several investigations and advancements have been conducted in the field of desalination, aiming to establish highly efficient and economically viable systems. Seawater reverse osmosis desalination (SWRO) is well recognised as the predominant technology because of its relatively low energy consumption. Nevertheless, the design and execution of SWRO is complicated, and several factors contribute to optimising its effectiveness and mitigating the associated issues. Each process and subprocess in a SWRO desalination plant relies on the output of the previous system to deliver high-quality results, efficiently, and with minimal environmental impact. There is a lack of a holistic approach to the design process of SWRO desalination that take all design factors into considerations. This thesis presents a methodology for assessing system design and selection under changing conditions, elucidating trade-offs between capital and operational costs, environmental impact, geographical features, and the associated limitations of each process. In addition, it assesses the suitability of a design according to these specific criteria. To achieve this, a suitable methodology for SWRO system evaluation is necessary. To address this challenge, this research proposes an ontology for complex and holistic analysis by assimilating data from all subcomponents and representing their interconnectedness within a desalination system. The ontology represents standardised knowledge (terms, relationships and rules) related to all the major components and processes of SWRO desalination. Thus, the developed ontology facilitates and encourages reusability of data for a multitude of alternative configurations within the SWRO domain. Three case studies were used to demonstrate the capabilities of the ontology to effectively model complex relationships and constraints. However, a review of the literature has shown that integrating the life cycle cost approach offers a greater understanding of the actual cost of system implementation and significantly influences the decision-making process for plant design selection. A SWRO design and LCCA tool was developed to simplify system analysis in user-defined, site-specific scenarios. The included life cycle cost data were gathered from a diverse range of academic and industry sources, facilitating the development of a cost database that is both user-friendly and accessible for regular updates. The methodology was assessed by evaluating the design derived from the three case studies. This demonstrates the tool's ability to capture the engineering principles of these processes and to perform life cycle cost analysis. Furthermore, it demonstrates the influence of different pretreatment methods, water characteristics, and specific process choices on the total capital expenditure (CAPEX) and operational expenditure (OPEX) resulting in a more holistic and comprehensive understanding of SWRO as a highly complex and interdependent solution to water availability.