It's common to say “I see” when we understand something. And indeed, “seeing” in the Bible represents grasping and understanding spiritual things. So it makes sense that the eyes, which allow us to see, represent the intellect, which allows us to understand spiritual things. This can also be used in the negative, of course; the Bible speaks of people having eyes and refusing to see, and the Lord when He was in the world advised plucking out an offending eye. These represent a refusal to acknowledge truth, or being misled by falsity.

Water generally represents “natural truth,” or true concepts about day-to-day matters and physical things. Since all water ultimately flows into the seas, then, it follows that a sea represents a huge agglomeration of such natural truths -- usually all of the natural truth a person has, or all the natural truth a church has. Water in the sea mixes freely, and is easily stirred up by winds and currents. This is also true of the concepts we hold about natural things -- they are not all related to each other, and when relationships do exist they usually can change without damaging the concepts themselves. Many of the concepts are easily disputed, and arguments can arise like waves on the ocean -- generally with little effect other than a mixing of waters. But the sea also offers great bounty. We draw fish from it (spiritual food), float ships (doctrinal systems) on it, bathe in it (using true concepts to purify ourselves), and the water that evaporates from it and falls as rain (purer forms of truth that can attach to desires for good) makes life possible.