Deep Waters begins on Nisan's birthday. As she is getting prepared for her birthday celebrations, with the help of her mother Leyla and her sister Irem, she is shocked by a text message: a farewell from her best friend Ezgi who decided to leave Izmir. Surprised and confused, Nisan cannot make sense of what is happening. Ezgi, an introverted and shy orphan, is a student at the same university as her. When she goes to the station to stop Ezgi, she couldn't find her on the train. She was not at home either. Nobody knew where she was. While Nisan tries to understand what is happening, she is devastated by the news: Ezgi is found outside of the city, left to death. She runs to the hospital to find out that Ezgi is in a coma, four months pregnant. Stuck between life and death, nobody knew when she would get better. Nisan realizes that she didn't know anything about Ezgi, who hid her pregnancy from her. But there is something else that she doesn't know.