Though there are various theories, the exact reason is still unknown.
As per a recent study by IIT Kharagpur and Archaeological Survey of India, a weaker monsoon might have been the cause of decline of Indus Valley Civilization. Environmental changes, coupled with loss of power of rulers (central administration) of Indus valley to sustain the city life might be the cause (Fariservis Theory).
There might be resource shortage to sustain the population, and then people moved towards south India.
Another theory by Dr Gwen Robbins Schug states that inter-personal violence, infectious diseases and climate change had played a major role in the demise of the Indus Valley Civilization