The above question has a two part answer: 

Firstly, for your yacht.

According to the Harbour Master there is NO LIMIT.
That may vary for marinas, depending whether your account is paid up to date. This particularly applies in Rebak, where some people leave their boat in the water, or haul out and just pay a couple of months in advance and go home.
Then through whatever circumstances, it's left for an extended period, without paying any further rent. That's when the two year limit, (that some people have heard of), comes into play and Rebak will then want the account paid in full....
OR THEY WILL SELL THE BOAT TO RECOVER THE OUTSTANDING RENT.

Otherwise, if a boat is in the water, or on the hard and fees are kept up to date, a marina will not care how long you're there. In fact, as far as they're concerned - the longer the better. There are many examples of live-aboard people who stay permanently in marinas or free anchorages for many years without a 'length of stay' problem. However, these rulings can change and sometimes it's simply up to interpretation of rules by an official. If that's ever a problem, you can sail to Thailand and come back to start a new length of stay...whatever that may be.


Secondly, for your personal visa:

The second part of the answer is very different. Your personal length of stay is governed by your status at the time of entering Malaysia. Most times it's on the basis, for most foreigners, of being stamped in for a 90 day tourist visa or longer if on a MM2H (Malaysia My Second Home) program, or if the holder of a work permit.

Be aware that the 3 monthly "visa run" idea is now coming under a lot more scrutiny by Immigration and the days of just doing a quick two way ferry ride to Satun and back on the same day are numbered. At best, you may be told that "This is the last time" and at worst you may be told to stay away for several days or weeks/months before re-entering. At the moment it's a random 'case by case' situation and depends on which officer is on duty on the day.

And be doubly aware that 'overstay' of a visa is now being treated very seriously.
If in doubt on this matter, read the following letter with the title:

Don't Overstay Your Visa - Or You Will Go To Prison !!

    

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