The actress took over the role of Lucy Beale in January after producers decided to recast the character.
> Coronation Street leads Inside Soap Awards 2012 shortlist
Bywater beat Coronation Street's Natalie Gumede (Kirsty Soames), Emmerdale's Gemma Oaten (Rachel Breckle) and Hollyoaks actor Steven Roberts (George Smith) to win the award, voted for by readers of Inside Soap.
The 17-year-old was said to be "thrilled" to learn of her win and looking forward to collecting her award at the ceremony tomorrow.
"Hetti was so excited when she was nominated, so to have won has left her totally thrilled. She's worked hard over the last few months and has been involved in a number of very emotional and gripping storylines," a source told the Daily Star.
"It's never easy replacing another actor in a role but she's made it her own and really deserves the recognition. She's a sweet girl and everyone is really happy for her.
"This was a really tough category for her to win, especially given that it was Corrie's Natalie Gumede who won it at the British Soap Awards. I think a lot of people were expecting her to win it again. But this time it was Hetti and EastEnders' time."
Inside Soap editor Steven Murphy said: "This year Inside Soap readers have been voting in their thousands - and the competition is hotter than ever. I can't wait to reveal the winners - there will be a few shocks, I can tell you!"