Hard work and comparative linguistics, along with a whole bunch of other factors. More can always be said on the matter if anyone else would like to have a go at it; for the meantime, we can look at the case of Ancient Egyptian hieroglyphics with these previous posts;

• A sadly now-deleted user has an overview of the 'threads to pull' in reconstructing Ancient Egyptian pronunciation;
• u/ajshell1 has a look as to how it was done;
• and u/XenophonTheAthenian and u/CommodoreCoCo have a few comments on scripts and language here;

More material in next post because grrrr tag limit.