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Remains of Victorian houses and the foundations of a 16th century building are among the finds made during a redevelopment project.
The discoveries have been made during the excavation for the new Wellington Dock Navigational Channel for the Dover Western Docks Revival (DWDR).
The finds include the basements of houses that once occupied the promenade.
They were built around 1830 and demolished just after the Second World War following permanent damage by shelling.
Further discoveries include the remains of the foundations of The Pent, overseen by Thomas Digges around 1570, under the approval of Elizabeth I.
This was the first success, following many failed attempts, at making use of a natural shingle bar that often blocked the entrance of ships.
Josie Sinden, DWDR conservation officer for the Port of Dover, said: “The installation of these foundations would have been a scheme of national scale and caused an increase in the price of tax on beer and grain at the time to cover costs.
“The inspiration for this style of defence was taken from work carried out on Romney Marsh and included packing the shingle with layers of mud, silts and chalk – materials all in abundance around Dover.
"DWDR discovered that the technique used to construct The Pent was used extensively in the Benelux.”
The digging began in March and was guided by heritage experts Archaeology South-East (ASE).
Kristina Krawiec, senior archaeologist at ASE said: “The excavation of such a large channel provides a unique opportunity to uncover deeply buried archaeological remains and the sediments associated with them.”
"At a much lower level below the shingle a small wooden fence-like structure was uncovered.
"Its purpose is not yet known but it could be connected with fishing, an early try at a sea defence or an attempt to control the shingle bar."
About 250 timbers were also uncovered on the beach side of the excavation.
They formed a sea wall and acted as fenders for the ships to moor alongside.
The structure was recorded using laser scanning and will be removed and stored for analysis.
The £250 million DWDR is the single biggest investment ever undertaken by the Port of Dover.
It will provide a transformed waterfront for shops, bars, cafes and restaurants and a new cargo terminal and distribution centre.
It will also provide more space within Dover Eastern Docks for ferry traffic.