In a statement the HSE West said the clean up from Tuesday is now complete.
The hospital says at the moment it is not known how much Tuesdays nights flood damage will cost, but management do not expect these costs to be very substanstial as there minimal damage to the inside of the emergency department.
Management say the bulk of the costs will relate to the response to flood and the cost of drainage and clean up.
The investigation is still ongoing, and it is currently focused on identifying what caused the flood.
The hospital says the result of the investigation will be released in October.
After Tuesdays nights flooding further arrangements have now been put in place in response to that.
A drainage trench is in place to intercept surface water running from the main Kilmacrennan Road off, while there will now be a flood pump in the carpark of the hospital at all times.
Management say it is hoped that these measures will lessen the chances of a repeat of these weeks flooding.