Pebble-tables are fine for that, but don't leave a persistant record. Mostly when I hear "writing system" I think "linguistic writing system", a writing system for language, rather than "mathematical writing system".

But IIRC a number of writing systems started off first as mathematical record systems before developing to encode linguistic information. Maybe a good example is cuneiform, which started off as tally marks in balls of soft clay stored in jars, for tax purposes, which developed symbols for encoding what kind of goods were being counted. Quipu may be similar, with more nascent development as a linguistic system.