If i create a terrain and populate with an eco system is it possible to stop plants /trees etc from growing out of any water i might add later such as a small pond? I know i could paint them on but was looking for a more automated method many thanks in advance

you could have the material as a mixed material and then use a distribution map to place the ecosystems and the water, although im sure there are better options :)

On the terrain eco, click the Decay near foriegn objects box on the Density tab.  It should not populate under the water then. 

Yes that works rather foolish of me not to realise that water counted as a foreign object! thanks