We are in an era, whether some people acknowledge it or not, or Apocalyptic climactic change, so this sort of topic will come up time and again.
But regardless of 'reality' apocalyptic disasters for which the gamer has no answer are simply Bad Game Design. As posted, most gamers will simply turn them off and if that option is not allowed, turn the game off.
On the other hand, human transformation of the landscape and adaptation to changes is as old as human settlements. Almost as soon as people started planting crops, they also started digging channels to funnel water to those crops - primitive irrigation, followed by dams to cache water for irrigation, followed by lifting mechanisms and diversion mechanisms to put the water just where they needed it and nowhere else. This, in places, had the ultimate result of allowing so much salt and other minerals to precipitate out of the irrigation water that they poisoned their own fields for several years, in some places long enough to abandon primitive settlements and cities.
Which brings up a point of what I would consider Good Game Design - everything should have a price. You can cut down an entire forest (much of the Amazon today is, in fact, trees that were planted by humans for their usefullness - the distribution of plants in many parts of the area is NOT natural!) - but it will cost you: the Cucuteni cities, some of the largest Neolithic settlements anywhere, eventually had to move off the steppes of (modern) western Ukraine because every tree within walking distance of the cities had been cut down (probably for firewood) and with no wheels it was impossible to supply the cities with more of that necessity. Medieval Europe managed their forests much better, with coppicing among other techniques, but even they started running out of Old Growth big timbers for ship construction in England - managing forests for their products could, in fact, be its own 'mini-game' if the designers wanted to go into that much detail.
Among the People Modifications/Adaptations within in Civ timescale:
Numerous seaports went unuseable because of shifts in sealevels or the silting up of river deltas where they were located: the ancient port of Alexandria in Egypt, for instance, is now 15 - 20 feet below the water lebel because of sea level rise over 2000 years. Scarborough (of "Scarborough Fair") in England is one of several seaports that didn't survive into the Renaissance both because ships got too big for =the port or the port silted up and became unuseable by anything floating.
Rivers, most notoriously in China but also the Mississippi in America, can change their course completely as a result of seasonal flooding. That is not only an immediate disaster to everyone living anywhere near the river, but also a longer-term disaster as river trade routes also have to be re-routed or abandoned. China's Great Canal project, which eventually covered some 1600 kilometers, was both to extend river trade routes and also to try to 'fix' the rivers in their courses, and immense efforts were expended all over western Europe to 'canalize' and fix the courses of major rivers like the Danube and the Rhine to avoid seasonal disasters - and some of that effort is now breaking down as a result of extremes in the flow of those rivers.
People have not only chopped down large amounts of forest, they have changed the landscape in other ways: aside from re-arranging rivers, canals result in effectively new rivers, in China, Europe, and parts of the USA (The Erie Canal effectively provided a 'sea route' from New York City to the Great Lakes and all the way to Detroit and Chicago before the railroads and was a major reason why New York City far outstripped Philadelphia or Boston in growth in the early nineteenth century).
And finally, and to my mind the worst lacunae in Civ: People have re-arranged the landscape profoundly in the last 100 or so years by strip mining entire mountains, tunneling through mountains or under the sea, bridging major waterways and coastal inlets, irrigating vast stretches of deserts to provide almost entirely new agricultural regions (Central Valley in California for one example). There should be much more extensive 'terraforming' available to the gamer in the late game besides just building some Sea Walls here and there and the occasional tunnel. As far back as the 17th century the Netherlands 'built' three new Provinces by damming up and draining parts of their coast and a large part of Tokyo Bay in Japan is now Land rather than Water as a result of human actions: we should be able to Build Land as well as Excavate in on a multi-tile basis!
