Most of time in small boat like a kayak navigation is done by sight. In other words, you see where you want to go, point the boat that direction and go. This is not to down play the need for a good chart and a compass. These are critical tools on any small boat, but much of the time you don't need to be steering a compass course and once you are familiar with an area you don't need to consult a chart before every decision.
The first, but often ignored, aspect of navigation is just choosing where you are going. Making good decisions based on the weather and conditions is the foundation of safe boating. Determining in advance where is going to be safe and the places to avoid will go a long way toward ensuring a safe and fun boat trip.
Once you choose your destination the second part of navigation is assuring that you get where you had in mind. While this may be accomplished by sight when the land marks are close together, you need ways to assure that you are actually sticking to the plan you had in mind. Unlike walking or driving, where baring obstacles, moving directly towards a landmark pretty much assures you will get there, in a boat there a forces which may throw you off despite scrupulous attention to staying on course.
Safe kayak navigation requires close observation of the conditions and tools to determine how they will effect you or if they already have.
