You can get the boat to remain stationary as if it were anchored. It takes a little practice, I do it all the time.

When you approach the shore remain far enough away so that the boat remains floating free, even at low tide. Make sure the boat is at a complete standstill, no forward or rearward movement and the sail is furled. Then jump or swim to shore, the boat will remain where you left it, no matter the weather.

It is one of the mechanics of the game.