Keyword ability. A flooded site has a minimum of one water affinity (W). Therefore, it's a water site, though it still provides other elemental affinities, if any. For example, if a Humble Village was flooded, it would provide earth (E) affinity and water (W) affinity. It would be a water site and an earth site. If an effect 'floods' a site (e.g. Geyser), that site gains the Flooded ability for the stated duration. Since Flooded is an ability, effects that remove abilities from sites will also remove Flooded.