The sort of bacteria that make you ill have a very limited life expectancy in the open air. Take basic precautions for a couple of weeks, like washing well after a visit to the plot, and then forget it.
How much damage the flood does depends on how long the soil remains saturated. Most roots require air, and after about 24 hours of saturation, plants will begin to be affected. My problem this year hasn't been the floods themselves, which ran straight off, but the constant wet weather, and resulting saturation.
