The Quay area was remodelled in 1676. The wharf, built in 1566 with hewn stone blocks, known as ashlar, was replaced with a dock 6m wide and 50m long and a thwart weir. The Quay House of the 1590s, reputedly the earliest commercial port building in the UK, was rebuilt as a two storey warehouse with eight doors leading out onto the new lighter dock. The Customs House was built in 1680-1 [the oldest such brick building in the country]. The Port of Exeter had control of all ports between Lyme Regis and Teignmouth and at one time over 100 Customs staff were based there.

By the 1670s ships of 60 tons were docking at the Quay and by 1698 vessels of 200 and 300 tons. The Quay would have been alive with the movement of lighters carrying coal, timber, tea, coffee, spices, wines and spirits, as well as the huge volumes of bales of woollen cloth. At Topsham goods were transferred to vessels heading for Holland, France, Germany, Spain and Portugal, as well as the West Indies.