With the increased interest in the design and deployment of advanced reactor systems, a desire for simulation tools supporting system analyses of reactor operation and safety is rising. Molten salt reactors (MSRs), one of the advanced reactor systems, utilize liquid-fused salt fuel as both coolant and fuel. During operation, MSRs generate insoluble fission products, including noble metals and gases. The buildup of these species in the fuel salt presents safety concerns, as they may deposit on surfaces of critical components and produce excessive decay heat, causing the failure of system components. The timely removal of these noble metals and gases would ensure the safe operation of the reactor system. The dynamic nature of salt fuel systems, involving the generation, decay, deposition, and extraction of noble metals and gases, calls for robust species transport models to facilitate system analysis and monitoring and the design of efficient species removal components. This paper concentrates on the development of a computational framework for species transport consisting of multiphase transport model formulation, mass transfer between phases, numerical implementation in the MOOSE environment, verification through the method of manufacture solutions, and validation against experimental data from the Molten Salt Reactor Experiment. Integrating this framework into the System Analysis Module (SAM) code further enhances SAM’s capabilities for advanced reactor analysis in the future.