In medieval times, the River Lek became the main outlet for the Rhine, and the Oude Rijn silted up.

Ships were towed by horse and human power, using a towpath along large sections of the river, many parts of which have since been upgraded to roads or cycle paths.

Then it flows westward through Woerden where first the Lange Linschoten branches off to the south and then the Oude Rijn forms part of the city moats.

After Woerden, the River Grecht branches off to the north and the Oude Rijn continues through the towns of Nieuwerbrug, Bodegraven, and Zwammerdam.

In Alphen aan den Rijn, the Aar Canal joins the river and the Gouwe branches off to the south.

As prevention, around 1100 CE a dam with locks was built at the village of Zwammerdam, upstream at the border to Utrecht, an area reigned by German Emperor Frederick Barbarossa.

The organisation has been privileged in 1255 by Count William II of Holland and Zeeland as central coordinator of all waterworks in the area and later was given the name Hoogheemraadschap van Rijnland.

At strategic locations the Romans did build guarding-towers and border-guarding castella and castra, including: Laurum (Woerden), Nigrum Pullum (Zwammerdam), Albaniana (Alphen aan den Rijn), Matilo (Leiderdorp), Praetorium Agrippinae (Valkenburg), and Lugdunum Batavorum (Katwijk).