She was part of the GB quadruple sculls crew which finished strongly behind Germany and the Netherlands.
Rebecca Shorten's senior international debut for GB in the women's eight ended with a fourth place finish.
It was a disappointing regatta for Coleraine's Peter Chambers and Joel Cassells, who finished outside the medals in their respective classes.
After finishing third behind Poland and Germany in the first World Cup of the season in Belgrade three weeks ago Nixon, 23, was moved to the front of the boat to stroke the Great Britain quad alongside Bethany Bryan, Mathilda Hodgkins-Byrne and Jess Leyden.
it proved an inspired move as the quartet kept a fast pace throughout the race.
In the third quarter they caught and passed Poland, bronze medallists in Rio, and closed on the Netherlands.
They were just half a length down at the finish and this was a positive result looking ahead to the rest of the season.
The GB women's eight have no returning members from the crew that won silver in Rio.
In their first appearance of the season the new line-up, which includes 23 year-old Belfast woman Shorten, were second at halfway behind eventual winners Romania before being caught by the Netherlands and Russia.
Peter Chambers, 27, and Englishman Will Fletcher were hoping to push on from their win in Belgrade three weeks ago but they had no answer for the lightweight double sculls Olympic champions Pierre Houin and Jeremie Azou from France, who led from start to finish.
The Great Britain scullers were fourth and in contention at the halfway stage but faded badly in the closing stages to finish sixth as Ireland's O'Donovan brothers Paul and Gary, Rio silver medallists, produced their trademark fast finish to take silver ahead of Italy.
Cassells, 22, and partner Sam Scrimgeour could only manage fourth in the lightweight pair final.
The duo were defending their European title and Cassells was going for three in a row but they trailed Shane O'Driscoll and Mark O'Donovan from the start as the Irish pair set off at world record pace.
They held on to win gold ahead of Russia and Italy with Cassells and Scrimgeour missing out on the podium.
Ireland's excellent championships also saw a silver medal for Skibbereen's Denise Walsh in the women's lightweight single sculls.
Enniskillen's Holly Nixon has secured a superb bronze medal at the European Rowing Championships in Racice.