Abstract Water scarcity poses a significant global threat to sustainable development and education systems. This study examines the critical intersection between establishing sustainable learning environments in South African higher education institutions (HEIs) and the water scarcity challenges. Employing a qualitative case study approach with thematic analysis, we engaged 45 stakeholders, including undergraduate students and university management, to explore the multi-faceted effects of water scarcity on institutional sustainability, affective well-being, and academic performance. Findings indicate that the principles of inclusive and equitable education are undermined by the disruption of daily academic routines, hygiene practices, and overall student health caused by an inconsistent water supply. The research underlines the importance of sustainable water access, aligning with Sustainable Development Goals (SDGs), such as SDG 3 (Good Health and Well-being), SDG 4 (Quality Education), and SDG 6 (Clean Water and Sanitation). Stakeholder insights emphasize practical solutions, including establishing alternative water sources, implementing water-efficient infrastructure, and promoting institutional collaborations to guarantee water security and resilience in HEIs. Providing actionable strategies for addressing water scarcity in educational contexts, this research contributes to global discussions on sustainable development. It emphasizes the imperative of institutional and policy interventions to protect education in water-stressed regions, fostering academic success, student well-being, and sustainable urban futures.