The municipality of Alphen aan den Rijn also includes the communities of Aarlanderveen, Zwammerdam, and Boskoop.

The city is located in what is called the 'Green Heart' of the Netherlands, which is a somewhat less densely populated centre area of the Randstad.

Consequently, several Roman fortifications were located along the Oude Rijn, including castellum Albanianae in the centre of Alphen.

After recurring problems with flooding, especially in Utrecht and Leiden, the Oude Rijn was dammed at Wijk bij Duurstede in 1122, thereby making the Lek River the main branch of the Rhine.

A Jewish cemetery on the Aarkade was founded in 1802, but it was abandoned and razed in the 1960s, with the remains re-interred in Katwijk;[5] in 2012, after fifteen years of community activism by local historian Anke Bakker and CDA council member Alice Besseling, a monument was installed and the area turned into a city park.

In recent years, a large part of the city centre has undergone a full urban renewal.

This "masterplan" included the addition of a new public square next to the riverbank, the construction of a performing arts theatre/cinema, an upgrade of local shops and the creation of pedestrian streets.

On 9 April 2011, a gunman opened fire at a shopping centre in Alphen aan den Rijn, killing six people and subsequently taking his own life.

Trains which head towards Alphen aan den Rijn railway station are notorious for not always opening their doors to passengers.