The actress announced her departure from the show last month after five years of playing Zainab Masood, wife to Ganatra's character Masood Ahmed.
Ganatra told PA: "I really do miss her - we worked together for five years intensely and we had a really good rapport.
"I've known Nina for 19 years, so when you work that closely and get used to each other's working rhythms and suddenly she's gone you do see a big hole there.
"Nina's excited to do other things and I'm excited because this allows my character to evolve in a different direction."
In a current storyline, Masood is being tempted by younger woman Ayesha Rana (Shivani Ghai).
"It's nice to have a beautiful young lady chasing your character around Albert Square for a while," he quipped.
"Morally, whether he does the right thing, that's the question. We'll find out in a couple of weeks... Will he or won't he do the nasty?"