The Neolithic Germ Theory of Disease? Still, a reservoir is a good idea. To have water for drinks during the hot summer week (singular) when all gathered to lie on top the stones and tan?

But where's the restaurant? There's a Neolithic restaurant next to the Stones of Stenness. Where's Avebury's?

I'd like to think so too, but I do wonder just how much was understood about the nature of disease and infection. It was only in the 19th century that typhoid and similar diseases were understood to come from bad water.
I forget the details, but there was a pump in Soho that was infecting everyone in the area, but no one connected the pump water with the outbreaks. Then some chap whose name I should remember, drew a map of the area plotting incidents of illness. Only then was the pump identified as the cause.

Similarly with plagues and other horrors - it was the air and odours that were judged to be the cause - hence nosegays and sweet smelling herbs. Malaria means "bad air" and no one ever considered it had anything to do with mosquitoes and bad drainage.

So I doubt if Silbury water was kept clean for health reasons - they might have wanted it clean because it tasted better though.

I think that theorising that Silbury Hill was planned to have anything to do with drinking water is spurious. Oetzi had whipworm in his gut - or was it the eggs of ? - I'm not sure. Sheep are roughly the same size as people and their parasites rapidly transfer, even with close contact with their pasture. (A scary one is the lungworm, husk, which grows to the size of an earthworm in cattle). The two roundhouse sites, in my valley, are both very close to perennial springs - water dries up on the fells, in the summer, too. But the natural round hills, which had a similar purpose to SH, in the north, just occasionally have springs nearby. (They seemed to be used to watch the sun and moon rise behind). There are some fossils that have the same shape as these sacred hills - which are being passed over - and there has been no formal association of the shape of these hills, both natual and artificial, with the shape of cupmarks !

Till now ...