Pretty broad question in one way, or maybe narrow depending on how you define it? Maybe you can be more specific. There aren’t that many highly dense metro areas in SEA.
As far as SEA cities are concerned, the most heavily populated metro areas are Jakarta, Bangkok, Singapore, Ho Chi Minh city (Saigon) and perhaps Kuala Lumpur. There are a couple of others with ~4m pop in Indonesia and the rest are not really super dense.
Other than Singapore, SEA major cities are all along large rivers or have very large water catchment areas. And SEA gets lots of rain. Singapore gets around this by a lot of recycling, desalination and water imports from Malaysia.
Of all of the ones I mentioned, Jakarta (the largest by far) is probably the worst off wrt to subsidence partly due to groundwater extraction aided by poor underlying geology. So they DON’T deal with this issue very well at all. The next worse off is likely to be Saigon (Ho Chi Minh) and they too probably aren’t dealing with this very well.
The much bigger problem is that many river and groundwater systems are getting polluted by industrial, agricultural and urban discharge.
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