Environmental justice is the fair treatment and meaningful involvement of all people, regardless of race, color, national or ethnic origin, disability, gender identity or sexual orientation, or income, with respect to the development, implementation, and enforcement of environmental laws, regulations, and policies (EPA, 2022). Achievement of this goal will occur when everyone enjoys the same degree of protection from environmental and health hazards, and equal access to the decision-making process to have a healthy environment in which to live, learn, and work. Anecdotal evidence would suggest however that this is not achieved for Metro Manila. Laguna Lake has been the focal point of national development efforts for economic activities, including flood disaster operation of the metro. The use of the lake as a source of raw water for domestic supply has become more significant and critical over the past recent years with the aggravating condition of water scarcity in the country’s capital. In addition, the lake serves as an important flood-detention reservoir during the rainy season, with flow diversions from upstream Marikina River basin. With competing and conflicting water-users, and continued environmental degradation from anthropogenic-based stressors, Laguna Lake has been considered the most stressed inland water body in the country. This study presents a three-dimensional hydrodynamic study of Laguna Lake to understand the physical processes, including vulnerabilities, that govern and influence lake hydraulics for various water uses. Simulation results revealed a significant increase in lake salinity concentration for incremental increases in lake water abstraction rate, suggesting the need for regulation. A numerical experiment on bathymetric evolution also showed various Pasig River hydraulic discharge features and an increase in hydraulic residence time of the lake, enhancing the lake’s eutrophic vulnerability. Modelling analysis on the lake’s flood detention function on the other hand revealed varying shore-land flood inundation extents and recession durations for changing lake-flood detention levels that warrants the need to effectively manage the operation of the lake for flood detention so as not to cause excessive flooding to shoreland communities. Evidently, efforts to incorporate environmental justice into resource and flood-risk management should be leveraged beyond water resources management and disaster planning towards a better integration of vulnerable communities into our broader social and economic systems. Results from this study substantiate scientific information for outlining water management approaches and conservation strategies particularly for fast developing urban environments.