The actress's character Lucy Beale turned against her troubled father Ian earlier this year after he suffered a mental breakdown and disappeared for a number of weeks.
Lucy and Ian have managed to get their relationship back on track in recent episodes, putting an end to the tense scenes that Bywater shared with on-screen dad Adam Woodyatt.
Bywater told The Sun: "Adam is amazing. He can turn on the tears so quickly that I find it hard not to cry in scenes with him. In one scene I filmed recently I wasn't supposed to be crying, and I just burst into tears. The team had a word with me about it, but luckily it worked out okay.
"Another time Lucy was supposed to tell Ian to 'drop dead' during a fight and I started crying because I just didn't want to say the words to him.
"Lucy is a bit of a bitch and that wasn't the first time I haven't wanted to say the lines she comes out with. I always end up apologising afterwards."
She added: "Lucy has been really hard on Ian, but in the next few months they really build up a relationship and you see a much softer side to her."
Bywater added that she believes she has improved as an actress since she first took over the role of Lucy.
She said: "I look back at my first scenes in EastEnders and just cringe because they are so terrible. I wasn't acting very naturally at all. Most of the time on set you can't tell if people are saying lines or having a conversation because they are so natural in their parts.
"At the beginning I was constantly asking people 'What were you saying?' and they'd reply, 'Oh no, I was just reading my lines'. I'd always wonder why I couldn't do that. But I think it's something that you get better at - I've definitely got better since January."
EastEnders continues tonight (October 22) at 8pm on BBC One.