Before the Holy Roman emperor, before any count of Holland, people lived here. Settlement evidence dates back to 2900 to 2600 BC. In 1990 a skeleton from roughly 1300 BC was unearthed at the edge of town, and the nuclear DNA recovered from it is the oldest ever identified anywhere in the Netherlands. In Roman times a stronghold called Flenio may have stood on the same ground. Then, like much of the western Low Countries, the region appears to have been abandoned between roughly 250 and 700 AD. By 726 or 727 a small church had been established here and is mentioned on a list of properties that Willibrord, the Apostle to the Frisians, donated to the Abbey of Echternach. Vlaardingen had become a name on a piece of parchment again, a place worth founding a church around.

The Saint Thomas Flood of 21 December 1163 ended Vlaardingen's first growth spurt. The Counts of Holland moved away and development stalled. Town privileges arrived in 1273, granted by Floris V, but the next big disaster was wartime: in 1574, during the Eighty Years' War, the Watergeuzen burned the town to the ground on orders from William of Orange so that the Spanish could not take it. The destruction is the kind of detail history books mention briefly. For the people whose houses were burning, it was the work of years undone in a night, ordered by their own side. Vlaardingen rebuilt and pivoted, as Dutch coastal towns kept pivoting, to the trade that the sea was offering. In Vlaardingen's case, that meant herring.

For centuries Vlaardingen was a herring port. The fishing boats had specific names, evolving with the technology: haringbuizen first, then sloepen, then loggers. They went out to the North Sea, came back with the season's catch, and supported a town built around the harbor. The Grote Kerk, probably established between 1156 and 1164, stood over the marketplace. Beside it the Waag handled weighing duties, the Visbank handled the fish auction, and the Oude Lijnbaan was where rope makers walked their long straight lines making cordage for the fleet. The Aeolus windmill north of the old harbor still turns. The fishing boats stopped using Vlaardingen in the years after the Second World War. The Vlaardings Loggerfestival, named after the lugger style of boat, still happens every first Saturday in June. In 2003 the mayor renamed it from Haring en Bierfeest, the herring and beer festival. In 2015 the old name came back. People prefer the truth in the title.

The twentieth century brought heavy industry, and with it air that made schoolchildren sick. In the 1970s Vlaardingen was sometimes considered the most polluted city in the country. On one memorable day a high school had to close because the smog was too thick to teach through. Out of those years came an environmental movement strong enough to leave a mark on the political culture, and over the following decades the worst of the industrial pollution receded. Vlaardingen now sits between Rotterdam and Maassluis as part of the larger urban region, divided by the A20 motorway into a southern half on the old harbor and a northern district called the Holy. Ferries still leave from here to Felixstowe, Immingham, and Hull. The harbor that once housed herring fleets is now a marina and an open-air museum, the old boats preserved as the artifacts of a way of working that ended within living memory.

In the Emaus Cemetery in Vlaardinger Ambacht stand six headstones for members of the resistance group known as the Geuzen, executed by occupying German forces in March 1941. Nine more headstones beside them are symbolic, marking other Geuzen executed and buried elsewhere. Since 1987 the town has awarded the Geuzenpenning, the Geuzen medal, every year to a human rights activist somewhere in the world. The choice of the name is deliberate. The Watergeuzen who burned the town in 1574 were also Geuzen, fighting for an independent Holland against an imperial power. Vlaardingen has not forgotten that resistance and atrocity sometimes share a vocabulary, and that the people who fought for the town's freedom and the people who burned it once stood on the same side.