Disease will also be a factor with marsh (3C3), and jungle as well as flood plain. Disease can effect two ways:
*within a city, any "population" working in one of these squares has a chance to die each turn. This will reduce a city's population. I have never seen a city loose more than 1 pop. pt. per turn.
*units fortified in these terrains also has a chance to die. I have never seen workers die, but I have lost military units. I think they must be fortified.
I also wonder if the calculation for disease doesn't also have some time factor. I see a lot of disease in the earlier ages, but even before sanitation it seems that it happens less often as the game goes on.