It takes a bit of effort to take seriously Wednesday’s Dutch referendum, in which voters rejected the European Union’s trade and cooperation agreement with Ukraine. The turnout barely nudged past the 30 percent needed for the referendum to be legally valid; the vote was nonbinding; and the pact remains in force (it would take a unanimous vote by the 28 E.U. governments to suspend it).

Still, the implications for relations with Ukraine and Russia and for the future of Europe cannot be dismissed.. Organizers of the referendum acknowledge that Ukraine was not the real issue and that the vote was a way to express broad discontent with the European Union.

Even if the vote did not put the E.U.-Ukraine agreement in danger, President Vladimir Putin of Russia got a boost. It was Russia’s fierce opposition to the 2014 agreement that led Viktor Yanukovych, then president of Ukraine, to balk at signing it. That in turn led to mass protests in Kiev, Mr. Yanukovych’s ouster and the rise of a Russian-backed rebellion in eastern Ukraine. The Dutch vote was thus a chilling signal to Kiev that European support for Ukraine’s westward course may not be strong or united.

The vote was also another illustration of the anti-E.U. sentiments swelling across Europe in reaction to the refugee crisis and the economic crisis before it. The Netherlands has a history of euroskepticism — Dutch voters, along with the French, torpedoed plans for an E.U. constitution in 2005, and the anti-E.U., anti-Muslim Party for Freedom of Geert Wilders has a strong following. “The beginning of the end of the E.U.,” Mr. Wilders celebrated on Twitter after the results came in. Probably not, but the referendum should be recognized for what it is: an expression of discontent.