Time has run out for Nelson's rebel house boat owner who's makeshift home will now be removed from the harbour.

The Environment Court gave the man three weeks to remove the structure from the bay, and he's failed to do so.

The Nelson City Council will now dismantle the structure and and remove it from the sea, although a demolition date and time has not been set.

Port Nelson Harbour Master, David Duncan, says he is waiting for instructions from the Council on what to do with the boat.