In recent years, Molten Salt Reactor (MSR) technology has received significant attention. Its low pressure makes the MSR a low-risk option which, when coupled with its high temperature, makes it a highly beneficial choice for power generation and suggests the ease of integration with other systems such as desalination. It is worthwhile with the growing interest in MSRs, to develop a simulation tool that can predict performance in a multi-faceted MSR-based flow loop. This study focuses on MSR applications, namely clean water production utilizing a specific optimized combination of FLiNaK and supercritical carbon dioxide (SCO2) cycles. It addresses the growing worldwide need to decarbonize our energy production and simultaneously provide clean water. The results of optimized MSR-desalination configurations exhibit promising implications for the production of abundant amounts of clean water while also maintaining ample power supply to the electrical grid. They show that a design for a coupled MSR and desalination plant are not only possible but that the components and design are scalable for 50–250 MWth power input.