What caused the end of the Indus-Saraswati civilization? There are many theories regarding this

In The Wonder That Was India, A L Basham presented a dramatic picture of the decline of the Harappan civilisation. According to him, from 3000 BCE, invaders were present in the region. After conquering the outlying villages, they made their move on Mohenjo-daro. The people of Mohenjo-daro fled, but were cut down by the invaders; the skeletons that were discovered proved this invasion. Basham concluded that the Indus cities fell to barbarians “who triumphed not only through greater military prowess, but also because they were equipped with better weapons, and had learnt to make full use of the swift and terror-striking beats of the steppes.” Sir R Mortimer Wheeler claimed these horse riding invaders were none other than Aryans and their war-god Indradestroyed the forts and citadels at Harappa. But Basham was not that certain of the identity of the charioteers; he stated that they could be non-Aryans as well.[In Pragati: What caused the decline of Harappa?]

Marxist historians now say that there was no Aryan Invasion, but there was migration.  One theory says that tectonic events altered the course of the rivers causing the decline of the civilization.  Another says, the decline was caused by weakening monsoons. But can climate change be the primary cause?
The weakening monsoon theory is not new.

Around 4000 years back, a dramatic climate change happened across North Africa, the Middle East, the Tibetan Plateau, southern Europe and North America. In India, during that period, there was an abrupt shift in monsoons, which lasted two centuries. In general, if you observe the patterns of recent years, monsoons have strong years and weak years, but they rarely deviate far away from the mean due to the dynamic feedback systems. It is a self-regulating system, but there have been occasions when the anomaly has lasted for few decades.
But what happened 4,000 years back was truly unusual; it was an anomaly larger than anything the subcontinent had faced since in the last 10,000 years. A paper published recently by Berkelhammer was able to narrow down the exact time frame during which this shift happened and it coincides with the decline of the Harappan civilization. This new study does not depend on indirect proxies (like pollen data), but uses a direct terrestrial climate proxy from the Mawmluh Cave in Cherrapunji and hence was able to show an unprecedented age constraint.[In Pragati: What caused the decline of Harappa?]

Here is another one

The Arabian Sea sediments and other geological studies show that the monsoon began to weaken about 5,000 years ago. The dry spell, lasting several hundred years, might have led people to abandon the Indus cities and move eastward into the Gangetic plain, which has been an area of higher rainfall than the northwestern part of the subcontinent.

“It’s not high temperatures, but lack of water that drove the people eastward and southward,” Gupta said [Indus cities dried up with monsoon]

Now animal bones from Bhirrana have provided clues regarding the decline of the Indus-Saraswati civilization. To appreciate this better, we have to know where Bhirrana is and its significance.

Look at where Kalibangan and Dholavira are. Kalibangan is on the left bank of Ghaggar and is located at the confluence of Saraswati and Drishadvati. Dholavira is at the Rann of Kutch, which is not really a place where you want to settle down. There was a reason the people of Indus-Saraswati civilization did so: during the Mature Harappan times, people of Dholavira had access to the sea. If you trace the path of the Saraswati Paleochannel, you will see the connection between the two places. Also, if you trace the paleochannel towards  north of Kalibangan, you will see Bhirrana.

 The Ghaggar (in India)-Hakra (in Pakistan) river, referred to as mythical Vedic river ‘Saraswati’ (Fig. 1A) originates in the Siwalik hills, ephemeral in the upper part with dry river bed running downstream through the Thar desert to Rann of Kachchh in Gujarat3. More than 500 sites of Harappan settlements have been discovered in this belt during the last hundred years. Of these several sites both in India viz. Kalibangan, Kunal, Bhirrana, Farmana, Girawad and Pakistan viz. Jalilpur, Mehrgarh in Baluchistan, Rehman Dheri in Gomal plains have revealed early Hakra levels of occupation preceding the main Harappan period.[Oxygen isotope in archaeological bioapatites from India: Implications to climate change and decline of Bronze Age Harappan civilization]

Here is the impressive fact about Bhirrana: it is currently the oldest settled site in the Indian subcontinent. It was settled from around 7000 BCE and is located close to the Saraswati river bed.  It was not an urban civilization at that point. Like the other Harappan sites, it started out as pastoral and later had major farming communities. Eventually, the people there developed the usual Harappan urban entities: mud-brick houses, sacrificial pits etc.
A recent paper analyzed the drinking water component inside animal bones of cattle, goat, deer and antelope from Bhirrana. This was compared against the monsoon levels in the Arabian Sea and carbonate levels in two inland lakes close to Bhirrana. While monsoons intensified from 7000 BCE to 5000 BCE, it declined from then.  This correlates with data available from other sites in Asia. When such an event happens, it affects rivers like the Saraswati and the sites along its banks. That did not cause the end of Bhirrana; it continued and thrived for while. The residents of Bhirrana changed their crops to adapt. From wheat and barley, they switched to drought-resistant millets and rice.

 Because these later crops generally have much lower yield, the organized large storage system of mature Harappan period was abandoned giving rise to smaller more individual household based crop processing and storage system and could act as catalyst for the de-urbanisation of the Harappan civilization rather than an abrupt collapse as suggested by many workers. Our study suggests possibility of a direct connect between climate, agriculture and subsistence pattern during the Harappan civilization. .[Oxygen isotope in archaeological bioapatites from India: Implications to climate change and decline of Bronze Age Harappan civilization]

What this means is that the end was not sudden. It was slow. Rain reduced. Rivers did not get the rains it once got. The boundless, impetuous and swift-moving Saraswati which once flowed till the sea, no longer did so. Maybe there were tectonic movements which caused the rivers to go haywire and forced people to move elsewhere.