Been working on my friends newly acquired R53 Cooper S today. Compression tested, oil changed, supercharger removed and inspected. The issue has been found.
Pretty odd design but the water pump is driven off the supercharger. One of the bearings had play in it and there was no oil in the supercharger (well not where it should be). This has led to a very worn gear!
Replacement charger on the way.
Side note: someone put the sump plug in way too tight. Breaker bar was needed to remove. 🤔