Achieving urban water security, particularly in mountainous regions of Hindu Kush Himalaya (HKH), is a major challenge for sustainable development. Water security problems here in HKH are often systemic but governed by diverse factors with complex interactions among each other. Hence, this study attempts to examine the complex linkages between water security and urban management at a local level of two countries, namely Nepal and Bangladesh learning from the experience of India. The systematic study will (1) identify underlying geographical, climatic, institutional and socio-economic vulnerabilities, (2) assess their impacts on urban mountain communities, and (3) document current and potential adaptation mechanisms to strengthen water security. Unlike indicators-based water security framework, this study will consider perception-based measures applying a mix of participatory research methods namely in-depth interviews and focus group discussions. To collect and analyse data tools like problem and solution tree, seasonal calendars and participatory GIS will be seamlessly integrated into the study. The major outcomes expected from the study include an issue brief that will help in developing framework guidelines for policymakers to engage with local water users for greater collective resource management. The study will also facilitate the sharing of knowledge by exchange visits and train young researchers on linking science with policy through participatory research.