Use the RuneStone on yourself (Such as Unique Power Self Only, or just target your PC or portrait)
Use the option to Swim will be at or near the bottom of the list.
Choose any of the next options (The water currents have no effect yet until swimming transitions are complete, so they will all just enter the water)
Exiting the water:
Face the shore and again use the RuneStone exactly as before.
Choosing Swim and any of the next options.
Exiting the water by any other means (other means will be fixed to work with this) will leave you looking like you are 'flying', and the system may still think you are in water so anything you equip or drop would be subjected to underwater environmental conditions.
For anyone who has got stuck in 'flying' appearance there is a book in the PC Test Tools chest in DMFI Start
How do you get back to the DMFI area once you're in the city?
Right for situations such as this we add a name to the portal in DMFI Start, simply say 'StartRoom' to the portal in Tivook Inn or Mid Donnel (works until next update)