Unless otherwise directed or modified by species bonus, items, or spells, swimming speed equals a character’s movement speed, reduced by -5 ft while in water that is at least 5 ft. deep. Anything the GM considers more than "knee deep" should be considered 5 ft. in this way. There may be other conditions in which make 5 ft. deep water Rough Terrain, but the square on a tactical map should not provide both a movement speed penalty to Rough Terrain and a 5 ft. deep water tile; it should be one or the other and give players a chance to decide which penalty they want to contend with (as some of their abilities may overcome it).
Should there be a strong current, Strength Challenge rolls should be made against a DR at the GM’s discretion. Failure results in being pushed back -5 ft. in the direction of the current. After three concurrent failures, GMs are encouraged to make the player roll an additional Strength roll to see if they start to sink, being overcome by the current.