A scientist designs an underwater biosphere after severe climate change causes coastal flooding and category 5 hurricanes that flood coastline cities including New Orleans and much of Florida. Government fights people moving into it (don't remember why) and when people start moving into the Ark, the designer is fatally injured and his consciousness transferred to the Ark's computer. People live underwater for several generations before they are able to move back to the surface. Much of what isn't flooded turns into desert. Some people alter themselves to stay on the surface and evolve past the point of being human. There is at least one other biosphere or Ark that survives.
This is Ark Liberty by Will Bradley
From the Google Books summary:
In 2084, melting polar caps and burning rain forests force survivors to live in Arks, self-contained biomes. Against orders, Stefan Li staffs an undersea Ark with as many refugees as he can before its ports are sealed. When Li is killed, a computer genius transfers Li's persona into the Ark's computer net--and Li becomes the Ark.