How is the direction chosen when landing a seaplane on water?
Here is a nice little article on it. But in general the small waves on the water will curl with the wind and can even be used as a wind indicator. For calm water you can obviously chose your direction based largely on wind (but if the water is very calm there is likely little wind). Obstructions will play into choosing direction as well and it is advised to overfly the intended landing area before touching down. As for rough water landings the article states 


  It is impractical to describe an ideal rough water procedure because of the varying conditions of the surface. In most instances, though, the approach is made the same as for any other water landing. It may be better however, to level off just above the water surface and increase the power sufficiently to maintain a rather flat attitude until conditions appear more acceptable


Your elements are (in no particular order)


Obstacles 
Wind
Landing Area (you need enough distance to actually land same as a paved strip)
Possible Rough Conditions 


You must also keep in mind where you can actually land a seaplane. Not every body of water is legal to land a sea plane in (emergencies aside). You may want to check out this recently released book on arguable the first guy that flew a seaplane around the world.