From the 2nd half of the 15th century there was a two-hundred-year period of political stability and a time of substantial economic development of Włocławek, stimulated mainly by the trade activities along the Vistula River. At the height of freight traffic, the customs chamber was created on 14th June 1520 by King Zygmut Stary/ Sigismund the Old/. It handled about 2,000 ships a year. This contributed to the growing importance of local trade, focused on fairs and city fairs.
An important event in the history of the city was the establishment of the first seminary in Poland in 1569. At that time, there was also a development of the cathedral school, and the bishops of that time became famous for their patronage of art and science.
In 1577 Bishop Stanislaw Karnkowski granted a privilege to a suburb called the New Town. It was located between the present Brzeska and Królewiecka streets.
The period of stabilization ended with the Swedish Deluge. The army of the northern Polish neighbor captured Włocławek on 29 June 1657. They looted and burned the town and murdered some of its inhabitants. The defeats were complemented by the destructive actions of foreign armies during the Third Northern War (1700–1721). Once again, the Swedish army together with the Cossack troops invaded the city. In 1769, Russian troops fighting against the Bar Confederation army plundered and occupied Włocławek. Similarly, in 1771-1772 the Prussian troops repeatedly requisitioned the town and imposed contributions on the city’s inhabitants.
Despite the attempt to rebuild the city by the Commission of Good Order in the years 1787-1788, the end of the eighteenth century was marked by regression and decline. In 1793. Włocławek, along with the entire Brześć-Kuyavian Voivodeship, came under the Prussian partition and became part of the province of South Prussia.
Participation in the Kosciuszko Uprising of 1794 marked the end of the Old Polish period for the city. The defeat of the uprising led to the Third Partition of Poland and sealed Prussian domination. From 1796 – because of the secularization of church property – Włocławek ceased to be the property of bishops and became a royal town.
