This is dependent a bit on the time period in question.

A fort in the eras before gunpowder is typically a standalone defensive structure - think castles or permanent fortified Roman encampments. In later years, forts are often associated with city defenses or as points of frontier defense. Although forts may exist in a defensive network in these later years, they are still independently defended. Fort is also a general shorthand for any fortified position in any era.

"Citadel" has a much clearer meaning. A citadel is a strongly fortified defensive point that serves as a last line of defense and final refuge for a city garrison. These were ideally built in such a way that one could not hold a city without reducing the citadel, which could be exceptionally difficult to do. After the advent of cannon and star forts, a city's citadel was the largest and strongest fort in a city's defensive network, usually the place from which the defense was coordinated.