People have speculated that it must be difficult to paint water. Of course it is, I wouldn't try otherwise.
No reason to assume it's intrinsically different to any other theme though.
It's down to knowledge, experience and affinity with the subject, primarily observation of shapes, patterns, rythms, colours and movements.
The reproduction of these elements is coloured by an emotional response which finds it's way through to the painting in mysterious ways. I don't know how this happens but will facilitate it by balancing considered and intuitive processes.