Two factors are exacerbating the flooding risk to the city: global sea level rise and subsidence. In short, sea is rising and the city is sinking. Like other cities built on river deltas, the sediment beneath the city is compacting over time. In a natural setting, this compaction would be offset by the deposition of fresh sediment at the surface, but the rivers feeding the lagoon were diverted in the 1500s. As a result, the land surface is sinking, and the salt marshes are suffering for it.
I won't spoil on how exactly water is being used solve Venice's water problem.