One game I loved as a kid was Venture Africa. It simulates a lot of the plant and animal interactions of an ecosystem and allows you to build your own. It’s old but it’s pretty cool and I still play sometimes to relax. I’ve recently gotten a couple of my friends into it too. There’s a sequel called Venture Arctic that I never got until recently. It’s fun too, but a lot different. It incorporates things like seasonality and climate change so that’s neat.
Zoo tycoon is a classic of course too - not a lot of ecological stuff but I would always use it to build sanctuaries. ;)