According to Legacy: The West and the World, by Garfield Newman, The was always a chief city in the dutch trade scene. Bruges served until 1500 when "its rivers silted" as in they were no longer usable due to being blocked with silt, harder for ships to go through, ships go elsewhere. Then until 1585 it was Antwerp because of "war and politics" (will check what that means right now) moved the trade capital to Amsterdam.

Edit: By war and politics he refers to the Dutch revolt, also known as the 80 years war. In 1576 the Spanish razed the city in what was called the Spanish Fury, on top of this trade with Spain was stopped due to the war and the city was besieged and captured in 1585. After this many of the protestants in the city moved to Amsterdam and other areas in the modern Netherlands. This decline in population, lack of trade and devastation by war caused Antwerp to lose its position as trade capital of the lowlands.

Iam sorry in advance if I cant really pinpoint a reason why Brugge declined, but i can tell you why first Antwerpen and later Amsterdam took its place as the most important centre of trade in the low countries.

In the 15th century we gradually see Antwerpen growing as a city and becoming one of the bigger cities within the Duchy of Brabant, it becomes a bit of a rival of Brugge but does not exceed it yet. At this point the primary international trade good that was traded there is English cloth. The next phase and why Antwerpen rapidly grew as an important centre of trade was that it became a refuge for the Jews from the iberian peninsula. In 1492 the Jews were expelled from Castile and Aragon, and in 1496 they were expelled from Portugal. These refugees brought with them the knowledge and connections to set up trade with the east. From 1453; the fall of Constantinople, Spain and Portugal practically had a monopoly on the import on spices to Europe. So when this group of refugees who were expelled from those countries sought refuge, they found it in Antwerpen.

The reason why they were able to settle there and not in Brugge is political. The cities of the Low Countries were incredibly politicly strong, and the Lordships where very decentralised. All cities had a vast repertoire of unique rights, and being a citizen of a city gave you a lot of protection. So allowing a person or a group to settle in your city and allowing them to practice their trade is a big political decision for the leaders of that city.

These refugees combined with the substantial capital the merchants of Antwerpen already had, became a very successful combination and Antwerpen grew to a hub for the extremely lucrative spice trade, being able to undercut the prices of the spice from Castile and Portugal.

This all changed when the Dutch Revolt broke out. Both Antwerpen and Brugge took part in the Dutch revolt on side of the northern Netherlands and later signed the Union of Utrecht in 1579 and NOT the union of Atrecht. Unfortunately Brabant and the cities in the border region, between what would become the Dutch Republic and the Spanish Netherlands, got by far the worst of the fighting. One of the major reasons why Antwerpen declined is the Sack of Antwerpen by mutinying Spanish troops in 1576. This was a catastropic event, it devastated the city.

This is were we see Amsterdam rise as the most important centre of trade in the Low countries, and for a while the world. The Dutch, and especially Amsterdam had already reigned supreme in trade in the North, being the primary traders in the Baltic sea after having pushed out the Hansa. During the Dutch revolt we see it grow as a power for trade with the East and other parts of Europe. This rise in power is directly linked to the stream of refugees coming from the southern Netherlands and the border region! The sack of Antwerpen, and the stream of refugees to Amsterdam it directly caused, gave the merchants of Amsterdam the know how and extra capital to greatly expand their trade. The biggest example of this being the start of trade with the east. Refugees from other parts of the southern Netherlands played an important part as well in this rise of Amsterdam. It is an often forgotten fact that the centre of the early Dutch Reformation was the cities of Flanders and Brabant. Which in the early revolt gave birth to several short lived Calvinistic city states. So when the Spanish rule over those regions was firmly re-established, the Calvinists had to move to the Republic.

The final blow came for Antwerpen when the Dutch Republic stopped trying to reconquer the city. They most likely did this deliberately. At some points during the war it is believed that the Republic was fully capable of taking re controll of the city but they didnt. Amsterdam, was to powerful within the Republic; they were by far the biggest city in the province of Holland, and Holland was by far the richest province in the Republic. Contributing over fifty percent of the money for the war chest. They pressured the Republic into not taking back Antwerpen, and therefore permanently doing away with their rival.

I hope this helped you a bit.

My Sources:

Friso Wielenga, Geschiedenis van Nederland.

M. Prak, Gouden Eeuw. Het raadsel van de Republiek, 99-124. (A very informative chapter that goes in dept on how the balance of trade shifted from the South to the North.)

Good Sources to read:

Jonathan Israel, The Dutch Republic: Its Rise, Greatness, and Fall 1477-1806.

Geoffrey Parker, The Dutch Revolt.

While both golfman and jw touch on reasons why Bruges fell into a decline, I feel like can add on a bit. For instance, while it's true that the silting of het Zwin made it significantly more difficult to reach Bruges, Bruges had always been a hard to reach harbour - but this silting is more of a consequence of Bruges falling in status rather than a cause. The city just no longer had the resources or the ability to prevent/repair/work around the silting. (Het Zwin had been having problems with silting for quite a while, even during Bruges' golden age - at first, this was countered by just off-loading cargo into smaller boats downstream. Later on when even those smaller boats could no longer navigate the waters, they even used carts and such. Eventually, either they couldn't keep this up anymore or it added to the factors which made Bruges unattractive as a trade port.)

More important were a couple of factors on a larger scale. One being the political developments in the area. Bruges had long since been an important port, even back when Flanders was just a county on the border between France and the Holy Roman Empire. It really started thriving under the Burgundians, however, and it seems its fate was partially tied to the fate of the Burgundians. When Charles the Bold died in battle in 1477, his daughter Mary of Burgundy turned to Maximilian I of Habsburg, an Austrian archduke, to protect her lands from foreign, mainly French, encroachment. Charles' sudden death had left the Burgundian Netherlands vulnerable, not only to attack from abroad, but also to internal strife. As jw mentioned, the cities in the Low Countries had traditionally been very politically strong. However, throughout the decades, those rights had been eroded bit by bit by the Burgundian dukes in their efforts to centralise power. Seeing both Mary's precarious position and their chance, the cities agreed to support Mary... if all their old local and communal rights and privileges were restored. Mary had no choice but to agree and gave them the Great Privilege.

This was all very short-lived, however. With the marriage to Maximilian, the situation in the Burgundian - now the Habsburg - Netherlands looked much better. Mary wouldn't live to see much of this, as she fell from her horse and died only a few years later, in 1482. Her lands were inherited by her son, Philips the Handsome, a four year old. Maximilian ruled in his place and Maximilian was very much not interested in honouring the Great Privilege, almost immediately abolishing it. The cities revolted.

Now, I should note that cities revolting or acting out upon getting a new ruler wasn't exactly uncommon. It was almost seen as a negotiation tactic at this point - after all, the count/duke/king had a personal relationship with each city/duchy/county/whatever (By which I mean that a title like the Duke of Burgundy could be fairly meaningless on its own and didn't give him any rights to, say, Bruges or Ghent or Antwerp. The Duke (or king or...) had a personal bond with each part of his empire and a separate title for each one) and while it was generally accepted that the heir of the former ruler would rule them as well, the terms of that relationship would be renegotiated to some extent. Normally, this involved giving some minor concessions, which would inevitably be renegged on during the new ruler's reign. However, Mary's extraordinary precarious position as well as the Dukes of Burgundy's attempts at centralisation led to the cities being able and willing to go all out with the Great Privilege. With such a major victory won and Maximilian's plans to return to centralisation clear, they knew this was the last time they could stand a chance to regain those old privileges.

In 1483, the Flemish cities, under leadership of Ghent, challenged Maximilian's regency of Philip by forming their own regency council. Philip being in Bruges at the time, Maximilian was forced to negotiate. This didn't go well. Luckily for him, the other cities and areas of the Burgundian Netherlands fielded allegiance to the archduke, in no small part because of how the Flemings behaved (among other things, trying to block Antwerp's trade routes). The first revolt against Maximilian ended after two coup d'états in both Ghent and Bruges in favour of Maximilian. The cities surrendered and Maximilian confirmed the cities' privileges... only to pretty much immediately go back on this and putting those privileges "under review."

Maximilian turned his attention back to warring with France and raised taxes in the Low Countries to finance this. This put a heavy burden on the local economy, which led to widespread anger - not helped by the lack of success in the war and the looting Habsburg troops. Ghent revolted again in 1487. From Bruges, Maximilian tried to negotiate with them... only for Bruges to join the revolt and take him as a captive. Holy Roman Emperor Frederick III, Maximilian's dad, joined the fray with 20,000 men and Maximilian negotiated his own release in return for the promise to return to the Great Privilege. A promise he promptly broke - again - upon leaving the city. This made him even less popular and now the revolt even spread beyond Flanders, with Brussels and Leuven joining the rebels.

Now, what's notable here is that much like in the first revolt, Antwerp firmly remained on the side of Maximilian, even raising a force to fight against the rebels. Bruges, meanwhile, was threatened by land by Frederick's army and by sea by a blockade by the Habsburg fleet, blocking off its trade. The revolt was crushed in 1492, leaving the Flemish cities weakened both in practical terms due to the ravages of war and the trade blockade, but also in terms of privileges. Antwerp, meanwhile, had been granted many privileges for their continued support of the Habsburg archduke and received preferential treatment in matters of trade. This made Antwerp much more attractive for traders than Bruges - and the city didn't really recover.