Most boat manufacturers fit as standard a device called a water separator filter which allows the water content to be drained off periodically. If fitted correctly these will be placed in the lowest part of the fuel system and are usually fitted with a glass bowl and drain tap. Following any lay up period these must be drained off. It is also a good idea to drain the fuel feed pipe to the filter-in the case of diesel installations condensation can produce large amounts of water in the fuel system. Try and fill up the tank at the end of the season to help avoid this problem.
Condensation also produces water in the engine oil and oil filters.
This problem increases when the engine has been periodically warmed up during the boat's lay up, and allowed to cool down during a chilly evening. Even with limited use, change oil and filters each season. It is not unknown for a neglected oil filter to rust through and leak out all oil, resulting in the seizure of the engine. Water is also an enemy of the boat's electrical system, and in particular the batteries. Keep the terminals clean and well-protected with vaseline.