Keyword ability. A flooded site has a minimum of one water affinity 
. Therefore, it's a water site, though it still provides other elemental affinities, if any.
For example, if a was flooded, it would provide earth 
affinity and water affinity. It would be a water site and an earth site.
If an effect "floods" a site (e.g. ), 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.