I should have realized that "System Data" referred to the "System Data" category, and wasn't just a generic term.
I don't think you can (or should) manage it directly, but sometimes you can try to figure out what is going on, and maybe to give the system a nudge in the hope that it will then clean up after itself.
What do you see if you go into Settings > (your name) > iCloud? I'm not interested in a screen shot that includes your Apple ID (please don't post that!) – just in the section that looks like this:
I doubt if it's going to turn up any "smoking guns" about you having so much data in iCloud Photos or iCloud Drive that synchronization keeps your Mac's local drive full to the brim. Especially since that Storage report already has categories for iCloud Drive and Photos – and the total of the numbers for those two categories is less than 1 GB.