The protesters began gathering at the city's Dam Square at 9:00 GMT. Despite the requests from the mayor's office to disperse, the crowd was only swelling in size.
The protesters marched 7 kilometres through the city, finishing at the Dam Square at 13:00 GMT.
The event's organiser was Michel Reijinga, who is responsible for similar protests against COVID-19 restriction in the past.
According to the Dutch public broadcaster NOS, citing the activist, about 60 groups took part in the march.
In August, the Netherlands announced that starting 20 September, a COVID-19 entry pass system will be used at restaurants, bars, cafes, events and cultural venues where more than 75 people are present.