I'll say some of the earlier Civilization games (especially Civilization II: Test of Time, Call to Power and Call to Power 2) had much more in-depth environmental mechanics than the more recent ones, though Gathering Storm for VI is a bit of a return to form.
Maxis' Sim Isle also comes to mind. It tries to simulate an island ecosystem, though the scenarios are all kinda balanced towards letting the player "sustainably" turn every island into a shopping mall or golf course, which is a bit of a bummer, because there seems to be a bit more than that to the actual simulation.
We also have the 2021 release of Imagine Earth, which tries to have an environmentalist message though I'm not quite sold on how it works mechanically, it really just feels like you're balancing a few different meters, and you can find magical (ancient alien) sources of power that let you temporarily pause or even revert climate change.
When it comes to a more traditional RTS, I might actually also suggest Total Annihilation. It doesn't really have an environmental model, but if you don't play on one of the metal maps (which gives you infinite access to metal all over the map), there are some interesting quirks in how it handles resources that makes you start recycling the wrecks of fallen units as well as clear the map of trees and rocks to power the war economy. It also has a rudimentary fire simulation going on, that like C&C will have forest fires spread across the map and damage nearby units. Like, it's not deep environmental simulation by the metrics of some of these other games, but few RTS games have anything even close to this.
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