Working waterlogged soil is never a good idea as it can destroy the soils structure causing severe compaction and is a pretty miserable task to try to perform to boot.
In irrigated agricultural land, waterlogging is often accompanied by soil salinity as waterlogged soils prevent leaching of the salts imported by the irrigation water.
The waterlogged soils of wetlands slow down runoff with nutrients, and the microbes in these soils filter the water -- taking out the nitrogen and turning it into a gas.