I had too many units in cities and I was losing gold every turn (this was in the campaign). The city screens give you little information about this really -- the stats are so poor right now in Elemental (or are hidden somewhere).
Anyway, I went to each city, dismissed armies, and before I knew it, I had tons of gold again.
Not saying this is your problem, but that was mine.
Last thing: Outside of running out of cash, there was no other side effect that I could see. People weren't dying in the cities, bill collectors weren't shutting down business, etc.
