I've been married 3.5 years and DH is in the Navy. He was already in when we met so it's all I've really known of our relationship.
Sea duty (when they're stationed on a ship) was a lot rougher than shore duty (when they're stationed on land at a base). We're on shore duty now after 3 years of marriage while he was on a ship. They deploy, go underway, etc. a lot when on a ship (at least the ship DH was on, was gone all the time). Now that he's on shore duty, he shouldn't have to deploy for 3 years. You alternate between sea and shore duty, 4 years sea and 3 years shore.
It can be hard, it can get lonely but it's totally what you make of it. We skyped when he was in port (once a month or so) and he called/emailed as much as he could. You honestly just learn to deal with it. You will get into a routine and it'll help to surround yourself with positive people.