Physics's don't know that only negative chargesnegatively-charged particles move. We can create ion currents on demand in many environments. We do know that the current flowing in a metal wire is negative chargesnegatively charged particles in motion.
As for how to determine that, you do a Hall effect measurement.
The measurement works by subjecting a current in a relatively wide bar to a magnetic field perpendicular to both the current and the width of the bar and then measuring the potential difference across the width. In this era of turn-key precision voltage measurements is easy enough to do in a high school laboratory if the students can follow the underlying arguments.