This is a single kanji with no okurigana, so it's using the kun'yomi reading. You don't know this reading yet, so here's a mnemonic to help you:
You go down to the harbor and speak the secret password me natto (みなと) to buy some fresh natto. Imagine the salty air hitting your face as you whisper, "me natto." Now eat that yummy natto by the water! Mmmm!
I would like to visit the port city of Veracruz.
Due to heavy rain, the road to the harbor is closed.
There was a mysterious ship drifting in the harbor.