Melina Andersson was early on with a tight group of five canoes that led the five kilometer long race in Racice.
For a long time it was Andersson who pulled the competitors, but just before the sixth and final lap, Zsoka Csikos, Hungary, went up to the top.
The Hungarian could hold on to the gold and the Swede was also passed by the Italian Susanna Cicali before Andersson crossed the finish line as third.
The bronze on the long distance was the 25-year-old's second at this year's European Championship. On Saturday, Andersson took silver in K1 1,000 meters.
Previously, Melina Andersson has several World Championship and European Championship medals on the two distances, but she is still waiting for her first individual senior gold in sprint.