The water's encounter rate will be turned down so no one gets too annoyed, but yes, there will be a decent amount of trainers afloat as well as on land and in cities. There are also land routes, so the game won't become super monotonous.
Plus, Tentacool won't be popping up in EVERY SINGLE route like in real Pokemon
EDIT: I would say only 30-40% of the region maps are actually water routes, so...
Surf will be available after the first gym, but its base power is reduced to balance it out early in the game.