Upvote:3
A Naval chaplain would serve his 'flock' in the same manner as the chaplain of a town would serve the townspeople. That is he'd oversee the religious aspects of their lives; confession, leading religious services, providing spiritual guidance and providing comfort to the sick and dying. With the exception of taking confession, Protestant chaplains had the same duties on their ships.
If they were assigned to a ship they would provide these services at sea during the voyages. A large warship could have a crew of up to a thousand men, so just taking confession (and keeping track of those who did/didn't) would be quite time consuming. Likewise, a chaplain assigned to a port would provide these same services to those people staffing the port.