Whilst there is some doubt about this, all experience and evidence indicates that it is the individual's residency status which influences the tax situation - not the geographical location of the yacht.
indeed it goes on to say:
When leaving a boat in a marina, say for the winter, it is probably sensible to leave it as very obviously de-commissioned. As a matter of good practice the log should show movements clearly and the time spent in Spanish waters. In the event of being challenged, the onus of proof is with the boat owner who is advised tot keep marina receipts, proof of air travel etc out of Spain. It is possible to have the boat precintado or sealed by the Customs as proof that it is not being used to follow the less than 182 day rule.

If you are right, and any foreign flagged boat kept in Spanish Waters for more than 182 days is liabile for the 12% matriculation, why would leaving the vessel out of commission make any difference?

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I agree why would leaving it out of commission make a difference? its still in Spanish waters for more than 6 months.

Moreover how does one decommission a boat which is gonna be in the marina afloat. You cant just take the "distributor cap off" :~) I say in the water as the Spanish do not have the facility to store boats ashore in the main, which would be one way of stressing thats its "decommissioned" Anyway ashore is still in Spain.

I dont know of anyone who in practice has acheived this