This paper explores the interconnection between thermal water resources and the sustainable development of wellness tourism in Bulgaria. Despite the country’s rich endowment of mineral springs and its long-standing balneological traditions, the sector faces challenges related to governance, environmental monitoring, and technological modernization. Through a comparative analysis of three leading wellness destinations in Bulgaria—Hisarya, Velingrad, and Pavel Banya—the study identifies critical gaps in resource management, regulatory enforcement, and access to green investment mechanisms. Field interviews with local stakeholders reveal mixed awareness and adoption of sustainability practices, with international tourists showing greater interest in eco-friendly initiatives than domestic visitors. Drawing on European best practices and policy frameworks, the paper proposes the establishment of national sustainability standards, digital water monitoring systems, and public–private partnerships to enhance both environmental responsibility and economic resilience. The findings support the argument that responsible thermal water use is essential not only for protecting natural heritage but also for strengthening Bulgaria’s positioning as a sustainable wellness tourism leader in Southeastern Europe.