ROTTERDAM, Netherlands—The Ever Given, the container ship that blocked the Suez Canal for days and disrupted global shipping for weeks after, pulled into port in the Netherlands early Thursday—ending a three-month saga that included a still-mysterious grounding, months of negotiations over compensation with Egypt and a consignment of summer womenswear too late for the season.

The ship, a 1,300-foot behemoth that carries 18,000 container boxes of cargo, is one of the world’s biggest seagoing vessels. For months, it has been one of the world’s best known, too, after its bow wedged into the Suez Canal’s eastern bank and its stern swung around and planted itself into the other side—blocking traffic in both directions.

It arrived at a Rotterdam container terminal early Thursday.

The ship originally set sail from Yantian, China, on March 8. It got stuck in the Suez Canal on March 23, where it spent a week, closing the crucial waterway that connects the Mediterranean and Red Seas. The passage accounts for as much as 13% of seaborne trade. A global shipping traffic jam ensued, with vessels anchoring on either side of the waterway. Other ships rerouted around the canal entirely.

A multinational team of some 600 engineers and sailors and a flotilla of the world’s biggest tug boats dug, then pulled, the Ever Given free. The ship then sat for months at anchor in a lake off the main Suez channel while its owner and insurers negotiated with Egyptian authorities over liability and compensation.

No accident report has been released, and the exact causes of the grounding are still unknown. The shipowner, charterer, Egyptian authorities and shipping experts have at various stages cited a series of possible factors, such as gusty winds, the vessel’s speed, judgment calls made on the bridge and by the Suez Canal Authority and the unique hydrodynamics of the narrow waterway.

Egyptian authorities blamed the shipowner and initially sought about $900 million in compensation. A preliminary deal was struck in June calling for about $200 million, according to people familiar with the deal.

The ship’s owner, Shoei Kisen Kaisha Ltd. of Japan, the ship’s charterer, Taiwan’s Evergreen Marine Corp. and its technical manager, Bernhard Schulte Shipmanagement, have declined to comment.

The ship weighed anchor in early July, headed for Rotterdam. It arrives too late, however, for many of the owners of the cargo on board. The vessel is laden with goods worth over $700 million but now months late. They include cargo from flat-pack furniture giant IKEA as well as Europe-bound apparel shipments for Tommy Hilfiger- and Calvin Klein-owner PVH Corp. and U.S. footwear maker Nike Inc., according to maritime tracking data.

The Ever Given’s troubles added to a series of events that had wreaked havoc on the world’s supply lines this year. A global chip shortage has beleaguered the auto industry. A cold snap in Texas hit plastics production. Containers, the metal boxes in which shippers pack goods for transport by sea, were already in short supply before the Ever Given scrambled the careful choreography that goes into making sure those boxes get to where they need to be.

“First, we had lockdowns,” said Ad Schoenmakers, director of Dutch freight forwarder Ritra Cargo Holland BV, whose customers include some smaller retailers with cargo on the ship. “Then, we had the Ever Given. The problems keep on coming.” He said a cargo of women’s summer fashion wear, which was supposed to have been in shops in April, will now have to be sold at a discount or stay in a warehouse for a year.

The ship will unload some cargo in the Netherlands before setting sail for the U.K. next month. Michael Shah, who owns Manchester, England-based catering distributor Easy Equipment Ltd., has $100,000 worth of commercial refrigerators aboard the ship. He was supposed to deliver one of them in time for a new burger joint that had planned to open at the end of a Covid-19 lockdown in the U.K. in late May.

Footage shows the Ever Given, the container ship that blocked the Suez Canal in March, moving again after the owner and Egyptian authorities struck a multimillion-dollar deal for its release, ending a monthslong saga at a critical global trade route. Photo: Mahmoud Khaled/AFP/Getty Images The Wall Street Journal Interactive Edition

Write to Benoit Faucon at benoit.faucon@wsj.com