Quick search though shows that it had been cut during at least one siege: https://en.wikipedia.org/wiki/Siege_of_Constantinople_(626). The key is that you don't have to destroy the entire structure during a siege too, you just have to break ti enough that water doesn't flow through anymore.
If you want to destroy a fort you might throw a dead animal in the well. If you plant to keep the fort, that would be a titanically stupid idea.
You can cut off food supply and restore it the moment your flag is flying. Hell, you can stand the wagons on a hilltop as part of negotiating a surrender. How do you divert a river and put it back on demand, with not even medieval technology?
Now I am wondering how Kurus handled this situation after he took Babylon.
The priests of Marduk in Babylon hated Nabonidis due to his abandonment of Marduk worship and making another city his headquarters.
It may have been more acceptable to the population to tell them that the Persians diverted a river at night and entered rather than saying the gates were opened by insiders.
On a small scale you can improve a stream by forcing the water to turn, using stones or posts driven into the water. If you have the ability to build a bridge, you have some ability to change the direction of the water.
In a floodplain or alluvial fan, all of the land is sediment from the river, which means that at flood stage the river has been everywhere and during a flood, or over geologic time periods, the banks of the river can shift. Oxbow lakes are old bends in the river that straightened themselves out.
In theory, if you had a city that was built beside the new banks of a river, you could go upstream and rechannel the river to an old course, either to expand the city or for nefarious purposes.
Also Babylon is, I think, a weird case anyway. If you look at a map of the Fertile Crescent, you see that the Euphrates forks, and it forks a LOT. And Babylon is located between two of the outer forks. Convincing a river that forks to chose another fork might just require some megalithic technology - throw some big rocks in until the flow rate slows rather than stops, and evaporation takes care of some of the rest. Or a phalanx of pilons all driven into the shadow of the next one up river (think geese in flight), which is how you divert a stream.
Even if the river doesn't stop, it might not have enough clear water in it to sustain a city under siege. Especially if you can get them to surrender before the next rainy season washes away all your hydraulic engineering.
Personally I have been to Istanbul and the only main reasons I can think of Constantinople did not fall much earlier because of its strategic location at the edge of peninsular surrounded by natural three water/sea barriers and its extensive aqueduct systems.
Imagine the constant barrage of attacks from the Muslim Empires namely Umayyad, Abbasid and Ottoman over the course of around 700 years. This is due to prophecy that Constantinople will eventually fall to the Muslim army and only the best army General will prevail[1].
The attacks and sieges was started during by the Umayyad Empire in 674 and only in the year 1463 Sultan Fatih managed to finally subdue Constantinople for good. The only other time Constantinople was conquered happened during the Crusades'sacking in the year 1204. The Crusade invasion is only temporary and only lasted until 1261.
But the turning points of both of the successful sieges are very different. The Fatih's armies do not have direct access from the mainland and they do not have significant number of Christian Latin supporters in the Byzantine Empire and inside the fortress, unlike the Crusaders. The Ottoman basically have to resort to clever maneuvers like literally carrying the warships over hills to overcome the multiple chains barracades along the Golden Horn. The Ottoman was victorious probably due to conventional military strength and tactics but oblivious on the importance of aqueducts system supporting the lifeline of the city. The Crusades however, probably much aware of the importance aqueducts to the city due to their significant number of local Christian Latin supporters and managed to strangle Constantinople out of its lifeline. The recapture of Constantinople from the Crusade to reinstate the Byzantine Empire, however, is much easier because the Nicaean Empire obviously know the city inside out and the aqueduct systems.
This is my pure speculation based on my limited readings and observations of Istanbul, and more research needed to verify the potential causes of the fall of Constantinople and the importance of its aqueduct systems.
[1]https://www.dailysabah.com/feature/2015/05/29/the-conquest-o...