McCartney is Commonwealth Youth Games in 2023 and European Under-23 gold medallist last year, but her bronze in Glasgow is a first senior international medal for the Enniskillen swimmer.
“I’m over the moon. I didn’t know what to expect coming in tonight, but I just wanted to give it my all,” McCartney told BBC Sport.
“It was the last individual race I have. I just wanted to end it off on a high.”
The two medals on Wednesday brings Northern Ireland’s tally in the pool to four after after Bethany Firth’s bronze medal in the 200m freestyle S14 and Barry McClements’ silver in the men’s S9 100m backstroke.
Five minutes before Wiffen won silver, Kate O’Connor secured Northern Ireland’s first gold of the Games as she won the heptathlon.
Gary Kelly and the duo of Chloe Wilson and Shauna O’Neill won bronze medals in bowls, and six Northern Ireland boxers are guaranteed medals after reaching the semi-finals.
In the men’s 200m freestyle, Jack McMillan finished in sixth place as Kai Taylor of Australia won gold.
England’s James Guy was second and Matt Richards of Wales took bronze.
McMillan was second after 100m metres but a surge from his Team GB team-mates was enough to surpass the 26-year-old and he finished in a time of 1:46.29 seconds.
After her medal, McCartney – along with Lottie Cullen, Alana Burns-Atkin and Grace Davison – finished seventh in the women’s 4x100m medley relay final.
In the men’s medley, the quartet of Patrick Johnston, Adam Bradley, Matthew Hamilton and McMillan finished in sixth place in the final as swimming came to a close at the Games.