From the reign of Emperor Claudius onward, between 41 and 54 AD, Roman cohorts were permanently stationed along the Oude Rijn. The river then was the Rhine's main branch, and the empire ended at its north bank. Albaniana sat as one fort in a chain that ran from the North Sea coast at Katwijk inland to the modern German border, part of what UNESCO now recognizes as the Lower Germanic Limes. The Romans built the first bridge across the Oude Rijn here, which made Alphen a commercial crossing as much as a military post. Germanic raids around 240 AD ended that. The fort fell out of use, the bridge collapsed, and the river kept flowing. In 1122, after centuries of disastrous flooding in Utrecht and Leiden, Dutch engineers dammed the Oude Rijn at Wijk bij Duurstede. The river the Romans had patrolled was downgraded to a quiet branch. It has not flooded since.

Through the Middle Ages, Alphen was a small fiefdom called Alphen en Rietveld, a name preserved today only in maps and local archives. In the 17th century the town came back to life as a hub for inland commerce. The Oude Rijn became a working river again, this time for barges rather than legionaries. Portions of the old towpath along the riverbank still exist, the kind of straight, grassy strip where men and horses once pulled cargo upstream by rope. The modern municipality is a 20th-century invention. In 1918 the small communities of Alphen, Aarlanderveen, and Oudshoorn were merged into a single town. Zwammerdam joined in 1964, Boskoop and Rijnwoude in 2014, which doubled the land area and pushed the population over 100,000.

You cannot walk the original Roman fort, because Alphen's main shopping street sits on top of it. But you can walk Archeon, an open-air archaeology park opened in 1994 just southwest of the town centre. Forty-three reconstructed buildings cover prehistoric, Roman, and medieval Dutch life, with costumed staff demonstrating everything from flint-knapping to Roman cookery. The Roman section includes a partial replica of the kind of fort Albaniana once was, complete with watchtower and the gridded barracks layout that made Roman bases identical from Hadrian's Wall to the Sahara. Across town the Avifauna Bird Park, which opened in 1950 and bills itself as the world's first dedicated bird park, holds parrots, flamingos, and birds of prey in a series of aviaries beside the Old Rhine. Together they make Alphen a town with two unusual specialities: birds and ruins.

Since the 1950s, Alphen has grown rapidly. A large neighbourhood went up on the north side, then another on the south side in the 1990s. Most of these residents work elsewhere; the town sits in the so-called Green Heart of the Netherlands, surrounded by the four big cities of the Randstad ring but not part of any of them. Alphen aan den Rijn railway station, just southeast of the centre, runs Sprinter services to Leiden, Utrecht, and Gouda twice an hour. The headquarters of the international information company Wolters Kluwer is in town. The city centre itself was largely rebuilt in the 2000s under a comprehensive masterplan: pedestrian streets, a new public square along the riverbank, a performing-arts theatre and cinema called Castellum that nods, by name, to the Roman fort beneath. Every March, the streets around the centre fill with runners for the 20 van Alphen, an international 20-kilometre race held since 1952; at the 2006 edition Haile Gebrselassie ran 1:11:37 over 25 kilometres, a performance that broke the existing world best, though it was not ratified by World Athletics due to missing drug-testing procedures.

Quirijn van Brekelenkam, the Dutch Baroque painter born in Zwammerdam in the 1620s, came from one of the villages now in Alphen. The poet J.C. Bloem was born in Oudshoorn in 1887. The classical contralto Maartje Offers, born in Koudekerk in 1891, sang on operatic stages across Europe before dying in 1944. From Hazerswoude came the tennis player Tom Okker, ranked world number 3 in 1974, and the table tennis champion Bettine Vriesekoop. The basketball player Arvin Slagter, born in Alphen in 1985, won an Olympic gold medal in 3x3 basketball in Paris in 2024. The town's most painful name belongs to the Jewish community that lived here before 1940 and was almost entirely deported and murdered during the German occupation. The old Jewish cemetery on the Aarkade, founded in 1802, was razed in the 1960s, and the remains were reburied in Katwijk. In 2012, after fifteen years of work by the local historian Anke Bakker and the council member Alice Besseling, a monument was installed and the site reopened as a city park.