My main strategy is to take the highest point, and build a pump there, so that there's grass around the water for calcification. I usually then put scrubbers at the very boundary of the circle of influence of the turbines. As for greenhouses, I try to build up some clean soil, then I perfectly piece together some greenhouses. For rocks away from the river, I usually dig a riverbed to the main river, for more expansion. However, since digging is quite costly (160 currency on normal), I usually do this if I have $400 or more. It helps to plan ahead, so place rivers near machinery, for easy packaging in stage three.
During stage two, I first find the best place to place the beehive. In later levels, the beehive is extremely valuable because of the lack of trees, sometimes you might have to restart the level for a good spawn. I first place a beehive in an isolated area, with plenty of grass, so I can burn it later on. I usually like to surround the area to burn with riverbeds or polluted/unplanted soil. Then, I plant everything around the river separating the forest, and I pollinate for the maximum yield. I have many times been forced to restart at this point, since sometimes the burning goes out of control. Wetlands are also a partial priority, since they are key to restoring the weather system.
When I start off stage three, I usually try to raise my money up with pylons first, since I'm always financially exhausted from finding places to place beehives. I like to place my steam plants on wetlands, since placing them on water can cause blockages. Another thing to note when constructing deconstruction pylons is, try to not let them eat up the pumps, or a section of the river might dry out. This is why I try to get the weather system up and running first, so that the rivers automatically fill in. In addition, the rain usually supplies me with money, so the weather is important. After the weather system is complete, I do everything with a drone from there, using the tree launcher when required.
That's my two cents of playing this game. It's my strategy, and it works most of the time. Although is is a bit luck-based.