When someone navigates a ship or an aircraft somewhere, they decide which course to follow and steer it there. You can also say that a ship or an aircraft navigates somewhere.

When a ship or boat navigates an area of water, it sails on or across it.

When someone in a car navigates, they decide what roads the car should be driven along in order to get somewhere.

When fish, animals, or insects navigate somewhere, they find the right direction to go and travel there.

If you navigate an obstacle, you move carefully in order to avoid hitting the obstacle or hurting yourself.

If you manage to navigate a difficult situation, you deal with it successfully.