Ice age and retreating glaciers created holes. And those holes filled up by the melt water of the glaciers.
The fact that they are still full of water is due to them being replenished by precipitation more than they lose water. If they would lose more water then what flows into them we would be speaking about the "land of many bone dry holes" in the famous Finnish desert.
I spent quite a bit of time on the Urton database in 2006. Would need to dig out the pre/post processing Perl scripts and see a more recent version of the database.
An area that would also be ripe for computational analysis is the texts from Spanish archives that are known to have been sourced from khipu readings. "Pärssinen, Martti & Kiviharju, Jukka. Textos Andinos. Corpus de textos khipu incaicos y coloniales. Tomo I & II" would be a good starting point.
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Thanks to the last ice age and retreating glaciers...