Compared to its predecessor not only the number and the function of ships have been considerably increased, but also the animation phases have became more detailed. Whereas in ANNO 1602 ship animation was composed of 8 steps representation in ANNO now takes place in 16 steps. In addition, wave motion is now also taken into account. The difference between trading vessels and warships is much more distinct than in ANNO 1602. Trading vessels have a higher cargo capacity and are slower and poorly armed.
Warships are fast, heavily armed and carry very little cargo.
The sails are either hoisted or reefed, depending upon the situation. Much as the production shops, ships have fixed operating costs and are subject to wear, making it necessary to occasionally return to the shipyard for maintenance. Fleet formation represents an additional special feature of ANNO 1503. The player can assign warships to escort trading vessels, for example. Fleet formation in ANNO 1503 also takes individual ship speeds into account.