The 30-year-old broke away from Sweden's Karin Johansson and Australia's Catherine McArthur at half way stage before crossing the line a second up on Johansson in Duisburg, Germany.
The Richmond canoeist placed fourth in Szeged, Hungary, in the same event but got it right in Germany, finishing in a time of 3:58.718.
"I was pleased with how last week went but I knew there were lots of things I could do a bit better so I really tried to work on them and it all seemed to come together," said Broughton.
"The three of us were level at 250 but then I managed to get away and get a bit of a gap."
Traditionally specialising in the marathon and 5,000m disciplines, Broughton has been putting in the hours on the shorter distance and was delighted to see the work pay off.
She said: "I have done a lot more 1,000m specific training this year and the training complements each other pretty well; the 5,000m, the marathon and 1,000m are pretty similar.
"Whereas last year I just turn up and raced, I feel a lot more prepared this year.
"I didn't want to have to race the semi so I thought I would go as hard as I needed to go to get a top three places. I had a pretty good race in the heat and I felt I had a little bit left in the tank which is always good.
"I also think it's more about getting race practice because I've hardly raced this distance internationally, so everything I do I learn a bit."