The megacities (MCs) with > 10 million population are counted 35 in the world. More than 60% of MCs are located in Asia and 70% of them are situated in coastal areas. Nutrients flux (NF) plays a significant role in maintaining ecosystem services and biodiversity in the coastal area. Quality management (QM) for water resources (WR) is important for the ecosystem as well as water use. In this project, coastal Asian MCs (AMCs) and associated cities are categorized based on their location (continent with a large river or island) and urbanization stage (US). The 1st US has a growing population, high dependence on groundwater for WR, and degradation of surface water quality; the 2nd US has a stable population, improvement of surface water quality by sewage treatment systems, but diverse groundwater pollution appears, and the 3rd US has population decline, growing dependence on surface water for WR, but expansion of groundwater pollution. Based on these criteria, coastal cities in Indonesia are as typical examples for island-1st US type, China as continental-2nd US type, Japan as island-3rd US type, are selected for study sites. For sustainable water use in AMCs and coastal ecosystem conservation, four specific subjects are proposed as A) Assessment of current WR and NF statuses considering vulnerability and resilience to water pollution; B) Reconstruction of NF history; C) Future scenario of WR and NF under climate extreme and human impacts; and D) Framework of QM for WR and NF.