The 30-year-old battled hard to come home behind China's Danni Song and home favourite Vanda Kiszli.
But when the Chinese competitor was later disqualified, Broughton was promoted to silver and could celebrate a fantastic weekend that also saw her come fourth in the K1 1000m.
"I feel I raced a lot stronger than I have ever raced before. It is good to see where I am against everyone else and to come back home with a medal in the 5km was the icing on the cake," she said.
Elsewhere, Jess Walker finished sixth in the WK1 200m and was delighted to blow off the cobwebs in style.
"I am really happy with this weekend, where I chose to focus just on the 200m. I felt I had a lot to work on after the heats and focused on the start for my semi. I didn't get it quite right again, but I nailed it in the final," she said.
"I was more relaxed going into the final and really enjoyed it. I still have a bit of work to do at the back end, but I feel I am up there as one of the fastest. There is a really fast group of about 15 women, all fighting for the medals which is really exciting."
Scotland's Katie Reid finished ninth in the WC1 200m A final. The women's crew boat made up of Emily Lewis, Deborah Kerr, Amy Turner and Hannah Brown also showed good early season form by finishing seventh.