The dock was built into the curve of the old city moat between 1704 and 1705, with a budget of 37,000 guilders and a plan unlike anything else in the Dutch republic. Perry shaped the basin to match the hull of a warship - narrower at the bow, wider amidships - so that the horse-driven pump would have less water to move once a ship had settled onto its blocks. At a time when dry docks were a recent invention and the Dutch navy had been losing warships to rot in its wet docks every winter, the geometry of the floor was a small revolution. The maximum length of any ship that fit was 180 feet, which the navy thought, in 1705, was enough forever.

From the start, the dock leaked. The engineers could not keep wet-dock water from seeping through the closure gates, and the floor was perpetually damp. The French invention of the ship caisson - a floating door that would have solved the problem - had been published in 1683, but the Zeeland Admiralty never installed one. By 1737, water was welling up beneath the gates. The naval shipworm bored into the timbers. From 1745, when a memorial stone records the dock's closure, until the 1830s, it sat almost unused. Plans were drafted in 1762, 1766, 1774, 1777, 1783, 1795, and again under Napoleon. None of them happened. For nearly ninety years, Perry's dock was a hole in Vlissingen that everyone agreed should be repaired and no one repaired.

Engineer A.E. Tromp finally got the commission in 1834. His rebuild lengthened the dock to 69 meters, installed a proper ship caisson, and added a Watt steam engine of 18 horsepower that could empty the basin in six hours. The total cost was 176,005 guilders and 80 cents. On 17 July 1838 the corvette HNLMS Ajax was the first ship to use the rebuilt dock, and for a brief, important window between 1849 and 1861 - when Willemsoord Dry Dock I had failed - the Vlissingen dock was one of only two dry docks the entire Dutch navy could use. In May 1864, the American Civil War cruiser USS Kearsarge ran aground near Ostend and limped to Vlissingen for repairs. Captain Winslow's ship sat in the dock for five days while hundreds of curious locals came to stare at the Yankee warship.

After the navy closed its Vlissingen base in 1868, the dock was sold to the De Schelde shipyard and entered a long second life servicing the early Dutch submarine fleet. HNLMS O 1 - the first submarine De Schelde ever built - was repaired here in 1906. The Polish submarine Orzel, the boat that would later make a famous wartime escape from Tallinn in 1939, was built nearby on the same yard. By 1939, De Schelde had opened a new 144.5-meter concrete dock and Perry's basin became known simply as Het Kleine Droogdok, 'the small dry dock.' It was declared a national monument on 7 March 1967. Seven years later, despite that status, it was filled in with earth.

Restoration started in 2010 when crews began excavating the dock by hand and machine, scraping out the soil that had filled it for nearly four decades. In 2013, Pieter van Vollenhoven officially reopened it. That August, the sail-powered cargo brigantine Tres Hombres became the first ship in thirty-nine years to use the dock. The name Dok van Perry surfaced in local media around 2005, an acknowledgment that the young English engineer's geometry had outlasted everyone who had ever doubted it. Today the basin is a small open-air monument near the center of Vlissingen, the stones of its sides still bearing the marks of the rabbets that once held John Perry's wooden door.