Generally speaking, we aren't really sure, however it wasn't a matter of them just disapearing over night. By the late Harrapan period, the cities were entering a slow decline. We begin to see an increase in mass graves, with forensic examination favoring internal rather than external violence, decreased amounts of food, and evidence of depopulation.

But to understand this, we have to understand the structure of the society. Previously, many archeologists thought that the IVC was relatively egalitarian, evidenced by the city layout having mostly equal distribution of housing and the large public buildings. However, recent theories have proposed that the civilization was not as egalitarian as it seems. Houses on the edges were more crowded and near where the sewage and waste would end up, so they would have smelled quite bad and been less resistant to disease. It is highly likely there was a fairly significant wealth divide where the wealth lived in the centre of the city and the poor on the outside.

The civilization was mainly agricultural, cultivated principally barley and wheat, though they also had sophisticated animal husbandry, notably domesticating the water buffalo and Zebu bull, both of which appear frequently on seals and seem to have been important as beasts of burden as well. Bronzework and later ironwork appear to have been somewhat sophisticated, though few good examples have survived. Ceramics were wheel spun and exceptionally well made, comproble to later Mesopotamian pottery. All the cities seemed to have been planned, rather than naturally expanding and a complex sewage system existed in many cities. A trade network existed between the civilization and those in Mesopotamia.

With all that in mind, what happened? Well, around 1900 BCE, the climate began to change. Previously, the cities were built along the now dried up Gaggar-Hakra, Indus is a bit of a misnomer, which would flood during monsoon season and provide a fertile floodplain for the growth of wheat and other crops. However, at some point during the late 20th or early 19th century BCE, the monsoon brought far less water than expected and the river began to recceed towards the Himalayan foothills. The Indus climate also became drier and cooler. The drought led to a decrease in crops making urban cities and artisans more difficult to support.

Looking at forensic evidence, we see an uptick in intercommunal violence consistent with famine and wealth disparity. Disease has also been suggested, though the mass graves found do not seem to support this, instead suggesting famine and violence. This factors led to depopulation of urban centres and a move towards rural populations with a focus on multiple types of crop. These populations moved farther south, especially into Gujarat. By the 16th century many cities were abandoned altogether and the ones that remained had moved towards an entirely agricultural economy. Writing seems to have been lost and ceramics were hand made rather than thrown and metalwork was unsophisticated.

Genetic studies indicate a strong relationship to Dravidians and a smaller relationship to Indo-Aryans. But these studies are a little over my head and I can't interpret further. They also, to my knowledge, have not included various Munda and other frontier people in the genetic surveys. Linguistic analysis is also pretty useless at the current moment as we have next to no idea of how to interpret the Indus Script and are still debating potential loan-words in other languages.

To conclude, environmental changes seem to be the likely candidate for depopulation, especially when combined with famine and violence, leading to a de-urbanized continuation of the civilization to the south and a move from artisans to full time agriculturalists. It is unclear exactly what happened to these agricultural communities, but it is likely they were absorbed into other populations. It is possibly they are the ancestors of the Dravidians or a branch of the same group.