As a card carrying member of the "been there, done that" club, every bit of the advice above is spot on! You need to inspect all of the floorboard area for damage. And while you are at it, look for one or more entry points for the source of the water - base of windshield, all firewall openings, A/C, ... you get the idea.
A wire brush wheel on a drill motor is great for breaking loose all the build-up. Vacuum out all the loose stuff, then hit it with Marine Clean followed by Metal Ready. Let it dry thoroughly for a few days before applying POR-15 paint. Here is my photo log of the process on my car. A tip from my brother-in-law: for non-critical areas, consider getting paint tinted to match your car color at a big-box store. I used my inspection lid as a source color. Since the floorboards are fully covered, they count as a non-critical visual area.
This is a pretty easy fix as long as no major damage is discovered. Remember - RUST NEVER SLEEPS!
Good luck.
Jim