The lower stretch of the Linschoten stream from Montfoort and Linschoten to Woerden silted up a long time ago and its flow was diverted through the Lek and Hollandse IJssel rivers, but at one time it was an important branch of the Rhine delta, connecting the Lower Rhine from Wijk bij Duurstede to the Oude Rijn near Woerden.

Then, in 689 king Redbad was defeated by Frankish Duke Pippin of Herstal in the battle of Dorestad and the Franks regained control of the area.

Liudger reports that Boniface preached in Wyrda, referring to Wierde, meaning that the place was on higher ground in the area.

Concessions were granted to settlers, who drained the bogs by digging dividing ditches beginning from rivers and streams and stretching about ¾ mile inland, thus creating the characteristic grid of fields still seen today.

The Counts of Holland expanded their influence, and by 1165 they built a fort called Svadeburg, near present-day Zwammerdam, about 7 miles to the west of Woerden.

Due to its strategic location on the border between the County of Holland and the Bishopric of Utrecht, various wars have been fought in and around Woerden by the various lords and ladies of these realms.

In 1300, John II, Count of Holland awarded the Lordship of Woerden to his brother Guy of Avesnes, who became Bishop of Utrecht the following year.

In 1311, Guy returned the Lordship to his nephew, Count William III, and Woerden remained part of Holland thereafter.

In 1410 John III, Duke of Bavaria-Straubing had the castle of Woerden constructed, and in 1510 the city hall was built.

During the reign of the Dukes of Burgundy, Philip the Good (1419–1467) and Charles the Bold (1467–1477) Woerden enjoyed an unprecedented period of peace, and by 1477 its population had almost tripled to about 1920.

Charles the Bold's death before the gates of Nancy was the prelude to renewed unrest, both with Utrecht and the duchy of Guelders, and the town suffered economic hardship because of it.

Johannes Pistorius Woerdensis (Jan de Bakker), a catholic priest, was the first preacher in the Northern Netherlands to be martyred as a direct result of his religious beliefs.

Jan de Bakker was a pupil of Hinne Rode [nl] (Johannes Rhodius), headmaster of St. Jerome School of the Brethren of the Common Life in Utrecht.

Rode was a proponent of Sacramentarianism, and in 1520 his father called Jan back to Woerden, perhaps out of concern about those heretic views.

After he returned he continued his preachings, and the conflict with the Roman Catholic Church was further aggravated by the fact that he broke his celibacy, and got married.

In the wake of iconoclastic riots that swept the country in 1566 a prominent citizen of Woerden, Warnaer Claesz, petitioned the city magistrates to introduce the Augsburg Confession.

Duke Eric was also instrumental in suppressing the ill-fated rebellion of Hendrik van Brederode, Lord of Vianen.

In 2015, the city's refugee centre formed the scene of a violent attack by 20 hooded people, bearing fireworks and pushing down fences.

The population centers in the municipality are De Meije, Harmelen, Kamerik, Kanis, Woerden, and Zegveld.