What kind of tree is it?

Generally, the reason to keep the graft above the soil level is so that the cultivar doesn't form its own roots and undermine the dwarfing and/or other beneficial aspects imparted by the rootstock.

The degree to which it is important to keep the tree from forming its own roots is probably determined by how important those rootstock characteristics are to you.

In some cases it hardly matters at all, such as when the rootstock is a seedling anyway. In other cases it could lead to disease, delayed fruit bearing, an enormous tree when a small one was expected, suckering, or any of a number of other undesirable outcomes.

You'll need to give more information about your particular circumstances to get a more specific answer.

chubasco:

You are planting in basins? I assume this is for the purposes of water retention, but many of us plant grafted trees on small mounds so that when they settle they do not do what yours are doing.

Keeping the graft away from the soil line also depends on the length of the rootstock stem below the graft. If you have lots of stem, it is easy to keep the graft several inches above grade; when the graft is close to the roots it is not so easy.

Maybe you should have another look at the way you are planting.

Don Yellman, Great Falls, VA

If it is pear or apple dwarfing rootstock you are having trouble with, then yes, you need to keep the scion above ground level. Or you could lose the dwarfing effect of your graft.

With plums, persimmons and most other fruits, I don't see a problem with the scion rooting below ground. Unless you are talking about cherry on Gisela rootstock or plum on Krymsk #1 rootstock.

Thanks all, I have 3 apple trees on semi-dwarf root stock also an early elberta peach, and 3 stanley plums. And Don, I have to use basins to facilitate watering, otherwise it would run all over the raised area of this small orchard. Lastly the previous owner planted the apples and the plums. He put in an irrigation system using pvc pipe. it is not a drip system. It has risers (1/2") with adjustable flow for the basins. I hope this helps. Brent