That should happen automatically (unless you've changed some settings)..

Eco-system will not populate near "unfriendly" objects (including water planes), unless the plane has been set to "eco-system friendly" - see above pic for example of "unfriendly" water plane. The ringed icon in the materials preview should be blue, not pink. (pink = eco-system friendly).
Also, ensure that "populate under foreign objects where possible" is turned off.

Of course, if what you want to do is have some parts of the eco-system (eg plants) being hydro-phobic, whilst other bits are hydro-philic (eg sea-weed) and yet more are neutral (eg rocks), well, that's a different kettle of fish altogether. And a lot more difficult..

PS - the kettle of fish should probably be placed without using the eco-system! :-))

Cheers,
Diolma