Historically a national navy operates from one or more bases that are maintained by the country or an ally. The base is a port that is specialized in naval operations, and often includes housing for off-shore crew, an arsenal depot for munitions, docks for the vessels, and various repair facilities. During times of war temporary bases may be constructed in closer proximity to strategic locations, as it is advantageous in terms of patrols and station-keeping. Nations with historically strong naval forces have found it advantageous to obtain basing rights in areas of strategic interest.

Navy ships can operate independently or with a group, which may be a small squadron of comparable ships, or a larger naval fleet of various specialized ships. The commander of a fleet travels in the flagship, which is usually the most powerful vessel in the group. Prior to the invention of radio, commands from the flagship were communicated by means of flags. At night signal lamps could be used for a similar purpose. Later these were replaced by the radio transmitter, or the flashing light when radio silence was needed.

A "blue water navy" is designed to operate far from the coastal waters of its home nation. These are ships capable of maintaining station for long periods of time in deep ocean, and will have a long logistical tail for their support. Many are also nuclear powered to save having to refuel. By contrast a "brown water navy" operates in the coastal periphery and along inland waterways, where larger ocean-going naval vessels can not readily enter. Regional powers may maintain a "green water navy" as a means of localized force projection. Blue water fleets may require specialized vessels, such as mine sweepers, when operating in the littoral regions along the coast.