Good geography led to the 16th century Low Countries being major trading ports (in particular Antwerp and Gent; later Amsterdam and other cities). They connected the North Sea and the Atlantic with the Baltics, running the trade of salt from Portugal, wool from Spain, grain from Scandinavia, herring from the Low Countries, etc. They benefited from Burgundian policy that supported them against the Hansa, and also the population shift of herrings from the Baltics into the North Sea in the 1400s.
The Low Countries also had very high levels of urbanization, and well-developed city governance with a credit system. In the 15th century this led to conflict between the state government and the city government, mostly when they were under Burgundian rule.
Later on in the 17th century, the Netherlands benefited from not only geography, but:
The demise of Antwerp as the trading center, following the Sack of Antwerp and the closing of the Scheldt.
The migration of non-Catholic merchants from the Spanish Netherlands.
Financial policy of the VOC, including internal monopoly to control prices, well-developed insurance policies, and industrialized ship production.
So it was not only geography, and I would say compared to other ports elsewhere in that region (Spanish Netherlands, British Isles), it was really the mechanistic developments that truly drove the prosperity.