The features of the palace depend on the time period. Currently visible is an accumulation of features over several centuries, the latest most dominant.

Thus, the palace was never exactly as depicted today. In addition, it has been reconsтιтuted in modern materials. The custom began in an effort to preserve the site from decay and torrential winter rain. After 1922, the chief proprietor, Arthur Evans, intended to recreate a facsimile based on archaeological evidence. The palace is not exactly as it ever was, perhaps in places, not even close, and yet in general, judging from the work put in and the care taken, as well as parallels with other palaces, it probably is a good general facsimile. Opinions range, however, from most skeptical, viewing the palace as pure fantasy based on 1920s architecture and art deco, to most unquestioning, accepting the final judgements of Arthur Evans as most accurate. The mainstream of opinion falls between.

From an archaeological point of view, the terms “Knossos” and “palace” are somewhat ambiguous. The palace was never just the residence of a monarch, although it contained rooms that might have been suitable for a royal family. Most of the structures, however, were designed to serve a civic, religious, and economic center. The term palace complex is more accurate. In ancient times, Knossos was a town surrounding and including the Kephala. This hill was never an acropolis in the Greek sense. It had no steep heights, remained unfortified, and was not very high off the surrounding ground. These circumstances cannot necessarily be imputed to other Minoan palaces. Phaistos, contemporaneous with Knossos, was placed on a steep ridge, controlling access to the Messara Plain from the sea, and was walled.[39] To what degree Minoan civilization might be considered warlike remains debatable. It can, however, be said that Knossos bore no resemblance to a Mycenaean citadel, whether before or during Mycenaean Greek occupation.

The complex was constructed ultimately around a raised central court on the top of Kephala. The previous structures were razed and the top was made level to make way for the court. The court is oblong, with the long axis, which points north-northeast, generally described as pointing “north”. Plot plans typically show the court with the long axis horizontal, apparently east-west with the north on the right, or vertical with the north on the top. Either arrangement is confusing unless the compᴀss points are carefully marked. About 5 km (3.1 mi) to the north of the palace complex is the sea at the Port of Heraklion. Directly to the south is Vlychia Stream, an east-west tributary of the north-south Kairatos. Kephala is an isolated hill at the confluence.

The Kairatos River reaches the sea between the modern port of Heraklion and Heraklion Airport to the east. In ancient times the flow continued without interruption. Today the stream loses itself in the sewers of Heraklion before emerging from under a highway on the shore east of the port. It flows down from higher ground at Arkhanes to the south, where part of it was diverted into the Knossos Aqueduct. The water at that point was clean enough for drinking. When it reached Knossos it became the main drain of the sewer system of a town of up to 100,000 people, according to Pendlebury’s estimate. Today the population is mainly to the north, but the sewer function continues, in addition to which much of the river is siphoned off, and the water table is tapped for irrigation. Looming over the right bank of the Vlychia, on the opposite shore from Knossos, is Gypsades Hill, where the Minoans quarried their gypsum. The limestone was quarried from the ridge on the east.