Some of his films explore the rise of religious fundamentalism, sectarianism and casteism in India, while others investigate nuclear nationalism and unsustainable development.

[1][2][3][4] Notable films include Bombay: Our City (Hamara Shahar) (1985), In Memory of Friends (1990), In the Name of God (Ram ke Naam) (1992), Father, Son, and Holy War (1995), A Narmada Diary (1995), War and Peace (2002) and Jai Bhim Comrade (2011), Reason (2018), and The World is Family (2023), which have won national and international awards.

[10] Virtually all of Patwardhan's documentary films have faced censorship from the Indian government, eventually being cleared after legal action.

[18] His 2011 documentary, Jai Bhim Comrade, was based on a police firing incident against Dalits at Ramabai Colony in Mumbai in 1997.

"[23] In December 2023, alongside 50 other filmmakers, Patwardhan signed an open letter published in Libération demanding a ceasefire and an end to the killing of civilians amid the 2023 Israeli invasion of the Gaza Strip, and for a humanitarian corridor into Gaza to be established for humanitarian aid, and the release of hostages.