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This study focuses on the process of updating and upgrading a large-scale legacy software system to ensure its compatibility with modern computing environments. The evolution and maintenance of legacy software pose significant challenges in software engineering, especially given the rapid advancements in technology, computing platforms, and dependent libraries. These challenges become even more pronounced when new systems are built upon existing open-source software, which may become outdated due to discontinued maintenance or lack of community support. In this work, we examine the problem from a sustainable computing perspective through the case study of the CyberWater project—an innovative cyberinfrastructure framework designed to support open data access and open model integration in water science and engineering. CyberWater is built on top of VisTrails, an open-source scientific workflow system. VisTrails has not been actively maintained since 2017, requiring an upgrade to ensure CyberWater’s continued functionality, compatibility, and long-term sustainability. This paper presents our work on upgrading VisTrails, including the complete upgrade process, tools developed and utilized, testing strategies, and the final outcomes. We also share key experiences and lessons learned, with a focus on the sustainability challenges and considerations that arise when maintaining and evolving large-scale open-source software systems in scientific computing environments.