The Sound Dues changed several times as time went on.
Eric of Pommern (king of Denmark) instituted the Sound Dues sometime between 1425 and 1429, and the rate was one English Noble for each large ship (smaller ships were not taxed). This was of course not popular, and several cities of the Hanseatic League managed to convince the Danes to reduce the rate for themselves.
King Christoffer of Bayern added a new tax to the dues in 1444, in the form of administrative fees to the duty office in Helsingør.
In 1472 King Hans added a tax for wine, and in 1475 a tax for salt was added. In 1508 there was also a change in the main Sound Due, so that ships with ballast paid less than loaded ships.
In 1517 King Christian II made a major change in the Dues, where ships now had to pay based on their tonnage (carrying capacity). It started out at one Gylden for every tenth "læst", which is an old measurment for ship volume. It varied according to the load and was not standarised between countries, which made things difficult. It can be approximated to 2.5 metric tons, but the actual measurment changed over time! In 1519 King Christian II also established some extra dues for each ship in order to pay for the lighthouse keepers.
In 1537 King Christian III changed things again, when he added a tax for copper, and in 1548 he changed the main Sound Dues to 1% of the value of the unprivileged goods. The admin fees and the lighthouse keeper fees were based on the ships tonnage, and there were still special dues for certain types of goods. In addition several treaties adjusted or removed the dues for various countries.
After this there were multiple changes to the Sound Dues, but it seems that it remained as a percentage of the value of the goods in addition to a fee based on tonnage and special taxes for some types of goods.
You can read more on the Danish Wikipedia page -
Øresundstolden - Wikipedia, den frie encyklopædi
and you can look up the actual records of the Dues that were paid here -
Sound Toll Registers online