It may be the case that a completely flooded planet is unrealistic (pace JG Ballard) but if my memory serves me aright, the end-Permian mass extinction (which was due to the planet over-heating) wiped out about 96% of all species. Game-wise, you could have successive "events" each of which removed one food from all tiles (and from buildings that provide food). That would have about the right effect, and certainly get everyone worried, even if they had settled well away from floodable coastal times.