make a port with palisades as far into the water as possible and put campfires protected from the elements around it or bonfires. Look for good places to build a port, usually the mouth of a river is a good spot. Also make sure to park your boat in water shallow enough that if it gets broken then you can easily recover the mats. Make sure the port is NOT close to your main base where you will be spending a lot of time at least 100~ meters away. At your port you should generally be in and out quickly loading or unloading that way you won't attract spawns and events at your port. Campfires/bonfires will generally keep most critters away from your boats.

If you really want to spend a lot of effort on a port you can make a "safe" port by building walls with palisades in the water just deep enough to let boats travel but not so deep that you can't surround the water area with palisades. It will take a tremendous effort tho and lots and dirt flattening the area underwater to the correct depth.