With the pressing issue of climate change, the protection of earthquake-vulnerable heritage structures in flood-prone areas has become an urgent and significant challenge. To address this, conducting vulnerability assessments is crucial, aligning with the objectives of United Nations Sustainable Development Goals 11 and 13, as well as New Zealand’s National Climate Change Adaptation Plan. This research introduced an index-based approach to evaluate the flood vulnerability of earthquake-prone heritage buildings in Auckland, New Zealand, taking into account the evolving climate patterns. Data collection involved document analysis, on-site observations, and mapping of ten earthquake-prone heritage buildings in Auckland. The results uncovered significant variations in 11 identified flood vulnerability indicators among the selected buildings, categorised under ‘Exposure’, ‘Susceptibility’, and ‘Resilience’. The type of use, surface condition, number of storeys, and finishing material of the facades were identified as the most influential indicators affecting the flood vulnerability of these buildings. This study’s index-based methodology presents a robust framework for making decisions regarding the preservation of earthquake-prone heritage buildings in New Zealand, particularly considering increased flooding resulting from climate change. Additionally, it introduces a quantitative intervention priority index that outlines and organizes the attributes of flood vulnerability assessment using different indicators.