The River Dee, which was a shipping route to the Roman city of Deva (Chester), had partly silted up by AD 383, creating a need for a port further downstream.

One was Lord Nelson's mistress, (Lady) Emma Hamilton, who was born in nearby Ness and bathed at Parkgate, apparently as a cure for a skin complaint.

Contrary to often-repeated legend, he did not stay in Parkgate before sailing to Dublin in November 1741 for the first performance of his Messiah (he travelled from Holyhead).

Sailing from Parkgate across the estuary to Bagillt was still possible in 1864, as there is a report of an accident in which the landlord of the Pengwern Arms and his brother were drowned when trying to land in rough sea conditions; three others survived.

The silting of the Dee has been accelerated by the deliberate introduction of the invasive colonising grass Sporobolus anglicus in Connah's Quay in 1928, resulting in the growth of extensive marshlands.

[11] During the Second World War, two of Parkgate's houses which contained cellars were converted into air raid shelters for public protection from German bombing.

A row of three houses – one formerly a butcher's shop – overlooking the anchorage was built in the early 18th century for the Mostyn estate; they are Grade II* listed.