What about CtP2/Civ4 like pollution system? Population and some buildings is produce some wastes. When it reach limit of city's "garbage storage capability" a dump is appear on random tile near city greatly reducing tile yield. Dump can be wiped out by workers. (it's looks like appearing and cleaning off of fallout on tile from nukes in civ5)
Some buildings will reduce pollution from production (like solar plants instead of nuclear plants). Some buildings will reduce polluton from population (like mass transit or garbage refinery). Some improvement will increase city's "garbage storage capability" (for example tile improvement "junk yard". When it worked by city it doubles "garbage storage capability" of the city.)
It feature is adds a one more challenge to industrial era.
Example of the realisation:
City's "garbage storage capability" 0/400
Population of 10 produce 1 waste each per turn = 10 waste per turn
Coal factory produce 40 waster per turn.
400\(40+10)=8 Then after 8 tours a random tile will be polluted reducing yield. (after that "garbage storage capability" drops to 0).
Fallout can be erased by workers, but workers use manpower. So unaccurate planning or avoiding ecology oriented technology will reduce either your yield output or your cash and capability to build wonders (you will waste it on workers to clean up this mess

)
P.s also can be added "production to ecology" function like "production to science" but it will reduce current "garbage storage capability" up to zero by 25% of current production yield each turn.

P.p.s some social policy or wonders also should affect on this