...if this was the only condition for "what city becomes a capital." Looking at Germany, there's Hamburg, Köln, München...all on nice rivers, but none of them were the capital of Prussia when Germany was first unified - since Prussia was the essential driver of that political process, Berlin became the capital. Something of a coincidence in the grand scheme of things, really.
Beijing has multiple rivers traversing the current municipal area, and they were dammed and directed into channels, or directed underground as the city grew (same for London, by the way - London has multiple historical rivers that are now entirely or almost entirely underground, not just the Thames)
I think the reason is simple, "Braindead" style. It's just that lizard folk prefer the marshes, so that's where we have to be.