Floods occurs most often Fall and Spring, w/November traditionally being the worst month. However, it could easily flood in May as the combination of rain + high tides + wind = aqua alta. San Marco is among the lowest lying areas of the city - so it gets the most flooding. If you are out walking around/sightseeing and you hear air raid sirens, that means that major flooding will occur in about 3 - 4 hours.

Should you bring boots: really a personal call. Its a tidal flood, the water goes up, the water goes down. If the flooding is so great as to require boots and they set up the passerelle (elevated walkways) then the sights in the Area Marciana will be closed anyway.