The modern theory that most of the stones were floated across has had doubt cast upon it by the discovery that at that time the Loch of Stenness (at least to the north) rather than being an open body of water was marsh with a few lochans (much smaller bodies of water).
Source : Radio Orkney for April 21st[bbc.co.uk/scotland/radioscotland/programmes/orkney/ online for the day shortly]