part of it is natural. We roughly divide day and night into 2 parts, so we already need to have considerations for halves.

It seems like base 12 was chosen simply due to religion. the zodiac defined the hours at night for ancient egypt, and the Goddesses of Seasons for Greece later on.

Minutes and seconds came because we let astronomers define them based on hours and movements of the sun along a dial. The time it'd take for a dial to traverse a literal arcminute and arcsecond (which is still a thing today). Though these times are very different from today's minutes and seconds. So we have math to thank for the base 60 measurements.