I would recommend using "muffs" on the lower unit,, If you have to run the engine out of water. Check your owners manual and see if they recommend using the flush port ONLY. Most will show the use of "muffs" while the engine is running, and the use of the flush port with the engine OFF.

Some say the Lower unit , and water pump assembly does not get the correct flow of water if you solely use the engine flush port, why chance it..Invest in a good set of Dual muffs and READ THE OWNERS MANUAL...