It's been a big feature in the later games. But it's been there since the start. Civ 1 had a simple mechanism where highly industrialized cities would create polluted tiles. You could clean up the polluted tiles with settlers. But if your settlers didn't clean it up quickly enough, there would be consequences. Plains tiles would turn into desert. Coastal tiles would turn into swamps.

In all the civ games it's always been manageable relatively easily

It was also in civ2 as a base feature.