The Australian heavy rail industry is investing in a widespread digital transformation that will deliver new enterprise system capabilities via the introduction and adaptation of new technologies, practices, and people. Rail enterprise systems are in a state of flux and stretch as new capabilities and improvements are implemented over time. They are characterized by complex technology acquisition and supply chains, variable, overlapping timescales, and numerous asset management and maintenance processes, all while dealing with the pressures of minimal system downtime, maintaining operability and safety, and providing a reliable service. The organizations within the enterprise delivering these capabilities will evolve over time to meet these challenges. A significant challenge exists in how to transform the enterprise system. It requires an understanding of the implications of its current constraints and plans for transition while managing the development of the future system and ensuring that the appropriate level of maturity is reached at the right point in the deployment. Organizational systems (a part of the enterprise system) consider the goals, behavior, and interactions of the humans within the enterprise system. This chapter describes the application of model-based systems engineering methodologies and tools such as SysML and the Unified Architecture Framework (UAF) to model the sociotechnical system as it evolves. While enterprise architectures are commonly used to manage the complexity and plan/design the strategic, operational, and technical views in detail, attention to the holistic organizational aspects is often considered to a lesser degree. The personnel view within UAF has been enhanced to introduce an integrated model of various human factors concerns (such as roles, competencies, training, workload, situational awareness, safety assurance, and organizational culture). This chapter, therefore, demonstrates how model-based systems engineering principles can be used to manage the complexity of the introduction of new capabilities from an integrated organizational standpoint with focus on human systems engineering principles.