The story of ''Silent Waters'', based on real facts, begins in 1979 when Pakistan, under President General Zia-ul-Haq's martial law, sets out on the path that will lead it to become an Islamic state. It weaves the tale of a woman's destiny with that of Pakistan's political development over a 25-year period.
Ayesha, a seeminly well-adjusted middle-aged woman never speaks about her past. Since her husband's death, she has devoted herself to her 18-year-old son, Saleem. This quiet, dreamy boy is in love with Zoubida.
Saleem becomes increasingly involved with a group of Islamic fundamentalists, neglecting Zoubida. Ayeesha is worried by her son's abrupt change of personality. Things grow heated with the arrival of Sikh pilgrims from India. One of these pilgrims is looking for his sister, Veru, who was abducted by Muslims in 1947. His search stirs up the past...