She was renowned for her empirical analyses of Harappan trade networks, social organization, and decline, authoring influential works such as Encounters: The Westerly Trade of the Harappa Civilization and Understanding Harappa, which established her as a leading scholar of the Indus Valley Civilization.

Her career centered on Harappan economy, social structures, and urban development, with a prolific output on overseas trade, political organization, urbanism, pastoralism, and the early state.

Together with archaeologist D Mandal, she reviewed the 2003 ASI Ram Janmabhoomi report, highlighting methodological concerns with the pillar findings beneath the Babri Masjid.

Beyond academia, she challenged established historical narratives, notably through involvement in the Ayodhya title suit where she contested certain archaeological conclusions.

Her work engaged with the politics of archaeology, critiquing ideological influences and Marxist interpretations during her time at JNU.

She emphasized archaeology as a rigorous, comparative science, focusing on early state formation, non-market economies, and the impact of historiographic approaches on understanding the past.

She re-evaluated established interpretations, including rethinking the Mohenjo-daro dancing girl as non-dancing and arguing for state-controlled production in beads and tools based on site distribution in places like the Rohri Hills.

Her fieldwork spanned sites such as Lothal and Dholavira, and she advocated mapping mound strata before digging to preserve data.

Her overarching philosophy treated archaeology as rigorous science, not national myth-making, with the past serving as social glue.

She rejected nationalist narratives linking Indus artifacts to Hindu continuities and criticized attributing universal traditions to Indus contexts as trivia.

Shereen Ratnagar, a leading Indian archaeologist of the Indus Valley Civilisation, died in Mumbai at 82 after a period of illness, leaving a legacy of challenging entrenched power and mainstream narratives.

Her research mapped early Harappan state systems and challenged the view that Harappans were uniformly peaceful, drawing comparisons with Mesopotamian contexts.