Europe’s largest port, Rotterdam, is counting down to Brexit. “In about 200 days’ time, if nothing else happens… we will need to supervise all the goods coming in and out of the UK market,” says Roel van ’t Veld, Brexit coordinator at the Dutch customs authority.

Hard Brexit or soft? Chequers dead or alive? Does “max-fac” make any sense? The feverish debate in Westminster is distant for officials in Rotterdam, who are working on the assumption the UK will leave the EU’s single market and customs union on 29 March 2019.

At the stroke of midnight, the UK will become another country to its EU neighbours. Rotterdam will have to run checks on 10,500 newly “foreign” boats. Officials expect a 30% increase in import inspections and a 100% increase in export inspections. Ferry operators warn of form-filling and delays. While a transition period could delay those changes until 2021, nothing is being taken for granted.

Companies are “spoiled” by the ease of trading within the EU’s internal market, van ’t Veld says. Take a Dutch company that makes ready meals for British consumers. Today it needs only a contract with a shop. In future, companies on both sides of the North Sea would need production location registration, an export declaration, exit and entry declarations and more.

“Instead of two pieces of documentation you would need nine additional documents,” says van ’t Veld, based on his reading of the UK customs bill. “In 200 days’ time, you cannot just send a ship, and if you don’t anticipate those changes, ships will not get through the gates.” (Since he spoke this month, more days have slipped by.)

The Netherlands will be one of the EU countries hardest hit by Brexit. Even under the “best-case” scenario of an EU free-trade agreement with the UK, it would lose 0.9% of annual economic output, worth €450 (£400) per person by 2030, according to the Netherlands Bureau for Economic Policy Analysis.

And when Brexit hurts, Rotterdam will feel the first pinch. Spread over a 25-mile-long area, the city supports 180,000 jobs and 3.5% of Dutch economic output. To prepare for Brexit, 928 extra customs officials and 145 veterinary inspectors are being hired, following a recommendation from the Dutch parliament.

Pieter Omtzigt, a Christian Democrat MP, who co-drafted the parliament’s report on Brexit, describes his message to the government: “Be prepared. Because Great Britain is running so late that you may run into trouble because there hasn’t been time to prepare things. This is a way too serious scenario.”

He would prefer Dutch public money were spent on 1,000 new teachers or nurses, he tells the Observer, but feels his country has no choice. “If, like the Netherlands, you earn more than half your money with trade, you understand that if the UK leaves the customs union, the work for customs and excise increases significantly. The Netherlands simply cannot afford a disrupted customs system.”

Fresh produce is exported from the Netherlands to the UK using just-in-time systems. Photograph: DutchScenery/Getty Images

Preparations are advancing. In November, Rotterdam will start test runs on new IT systems. Port authorities worry about the 35,000 small and medium-sized Dutch companies that trade with the UK and have never dealt with the paperwork that comes with buying and selling outside the EU. “If the companies are not well prepared, then we will be in deep trouble,” says Mark Dijk, manager of external relations at the port of Rotterdam.

The preparations underscore how unusual Brexit is: a move to put up barriers, rather than bring them down. Rotterdam’s “short-sea” shipping port used to have customs offices for checking goods coming from the UK. But they were dismantled after the launch of the single market in 1993. The space has gone. No one ever thought it would be needed again.

Hemmed in by railway tracks and motorway, Rotterdam has no room to expand its short-sea ports. Nor can it afford to slow down, says Marcel van der Vlugt, operations manager at the ferry company Stena Line. “Our business is running 24 hours a day, 365 days a year, so there is no space to slow down. There is only space to speed up the process.”

Brexit is not as simple as winding the clock back. The number of lorries passing through Rotterdam has more than quintupled since 1989, while “just-in-time” supply chains are far more intricate.

“The situation has changed since 1993,” says van der Vlugt. He was speaking on board the Stena Transporter, hours before it began its overnight voyage to Killingholme on the Lincolnshire coast, laden with fruit, vegetables and industrial goods.

Finely tuned just-in-time systems mean a British supermarket can order a crate of Dutch cucumbers at 8am and have them on the shelves before teatime. Many of the UK-bound lorries at Rotterdam are checked on to the ferry in 90 seconds.

I would like the UK to stay within the common market, but it appears that the UK prefers not to Pieter Omtzigt, Dutch MP

Stena Line, which runs four or five ships a day to British ports, is worried about delays to cargoes of fresh produce. “That there will be congestion, no doubt – to what extent, difficult to say,” says Annika Hult, the company’s trade director.

For some British politicians, fears over delay and bureaucracy are exactly why the EU should grant the UK an unprecedentedly generous post-Brexit trade deal. But this argument – a variation on the German carmaker thesis promoted by Brexit supporters such as Boris Johnson – has not found favour with the Dutch government.

In The Hague, unravelling the EU single market is seen as a bigger risk to the Dutch economy than Brexit disruption.

Rem Korteweg at the Netherlands Institute of International Relations does not see the Dutch government breaking ranks with the EU, not least because the Dutch have “massive concerns” about the economic playing field being tilted in favour of the British. “If there is an element of de-regulation in the UK, it could really introduce a competitive disadvantage that would harm the Dutch.”

The UK has a choice, believes Omtzigt. “If you do not have a customs union and a common market then you have checks on the borders,” the Dutch politician says. “I would very much like the UK to stay within the common market, but it appears that the UK prefers not to.”