Known as the “pearl of the Adriatic”, Dubrovnik has become one of the biggest tourist attractions in the Mediterranean. Its charming old town, array of Unesco World Heritage sites and sizeable port were always draws, but the new success of Game of Thrones, much of which was shot in the Croatian city, has made it a particularly popular stopoff point for cruise ships, whose passengers are told they can see the highlights in a single day.

Smaller boats or tenders take the passengers on to dry land, where they are typically bussed into the old town. Tours often start at the 16th-century Pile Gate, followed by a stroll along the Stradun to the city walls, entrance to which costs €30 (£27). Game of Thrones locations and Europe’s oldest pharmacy in a 14th-century Franciscan monastery are big pulls.

Last year around three million visitors descended on the old town, most of them having poured out of around 400 cruise ships docked in the harbour. Critics say they are causing long-term damage to historical sites, but with the livelihoods of 80% of the locals dependent on tourist traffic, some are reluctant to address the problems.

There is increasingly troubling evidence, however, of the dramatic effect the guests are having, not least on the kind of city Dubrovnik will be. Where once there were bookshops, bakeries, butchers, hair salons and markets, tacky souvenir shops and stalls now cater to the tourists. The boats themselves also burn huge amounts of fossil fuel, creating water, air and noise pollution, and severely affect the marine ecosystem.

A growing sense among city residents that tourism has become overtourism has caused the mayor to introduce tighter controls: during mornings just two ships can dock, with a third after midday. Next year a limit of 4,000 daily visitors will be allowed ashore, and in two years each will face a €2 tax.

Another proposal is for ships – which tend to leave their motors running so that fridges, air conditioning and other technical functions continue to operate – to be forced to draw their energy supplies from the Croatian mainland instead. The mayor’s argument is that the city should at least benefit financially from the presence of the ships, though environmentalists note that the stipulation won’t stop the ships from running the motors or address the ecological damage. Nor is there any detail about how these measures will be applied, or how to ensure cruise ship operators abide by the rules.

Meanwhile, in neighbouring Montenegro, another small city is facing a similar problem to Dubrovnik but is even more vulnerable. About two and a half hours along the coast, the tiny city of Kotor often has three huge ships docked in port, each staying for an average of 12 hours. The third most popular cruise ship destination in the Adriatic, Kotor expects a total of 500 cruise ships in 2019, bringing more than half a million people. “Compare this to 2003 when there were just 50 ships and 50,000 people,” says Vesna Mačič from Kotor’s institute of Marine Biology.

Kotor is even more at risk than Dubrovnik because Montenegro is outside the EU, so EU laws don’t apply. The city has no recognised marine reserves, ships can use cheaper oil containing sulphur, and there are no restrictions on noise, which is known to damage organisms such as fish, dolphins and turtles.

Kotor’s location – at the end of the Boka Kotorska bay, which is surrounded by large mountains – means gases emitted by cruise ships linger for longer, damaging local air quality. Fishermen and marine biologists also complain that the ships drag along the bottom of the bay, damaging the ecosystem, and that they discharge waste water, thus releasing foreign matter into the bay and further upsetting the natural balance. Flowering sea grass, clams and the rich seabed flora are said to have suffered as a result.

“The biggest issue is due to the huge size of the cruisers, meaning only one can be directly attached to the port at one time, and the other two or three on any given day have to be anchored further away,” Mačič says.

“This creates huge physical damage to organisms – sponges, coral, sea stars and others – inhabiting the muddy sea floor. On top of that you have the constant lifting and lowering of anchors and the movements of the ships, which affects light distribution and therefore the ability of plants to perform photosynthesis, endangering various types of algae and seaweed.” She wants to see cheap oil banned in line with EU legislation, the number of ships limited, buoys used instead of anchors, and tugboats turning the ships around.

In a country where the average salary is around €453 a month, however, there is little appetite for any major restrictions on tourists, who spend an average of around €40 a day. In Kotor, at least, most locals are resigned to the idea that the cruise ships are unlikely to go away.