Not Necessarily an Issue
There is not a guarantee that there is a problem with your charging system if the rectifier on your 1999 Suzuki GSXR keeps burning out. Splashing through water is very unlikely to have been the root cause of the issue.
Your era of Suzuki is unfortunately notorious for burned out rectifiers and stators. Whomever they were sourcing them through had a huge quality control issue. The TLR and TLS of that era had the same issue as did many other models. Essentially, the charging systems were junk.
Testing Your Stator
There are three yellow wires that come from your stator. They come out of the left side crankshaft cover and route into your sprocket cover and out along the cast bottom portion of your frame on their way to your rectifier. They connect directly to the rectifier. You can disconnect them from the rectifier and test them with a multimeter. Your first test will be static. The engine is not running. Be sure to disconnect from the rectifier and not just try and pierce the wires with the multimeter end. They are special wires and insulated a bit more, these are one of the few wires on the motorcycle that carry AC current.
Static Test Set multimeter to ohms and test between all the leads in pairs. The reading 0.1 to 1.0 max resistance.
No Load Test Dynamic Test Set your multimeter to AC Volts and start the bike. It should be cold. Have a friend hold the RPM's at 5,000. Test between the leads. You should see more than 70V. If it's below that, you may need a new stator. I would replace, but I'll get to that later.
Testing Your Rectifier
Your rectifier has diodes in it. Diodes are one way valves for electricity, think of a reed valve in a two stroke in-take. Since this is a three-phase charging system you need diodes to join the AC current into a single output and convert to DC. I could get more detailed but I want to keep it simple.
Rectifier Resistance Test Using your multimeter set to ohms connect the multimeter to the ends of each of the diodes and check the resistance in both directions. You should have low resistance in one direction and higher in the opposite direction. Generally, you will want to see 5 - 40 ohms of resistance in the forward bias direction, and infinite resistance in the reverse bias direction.
Procedure Attach the black probe (-) of the meter to the ground side of the rectifier (black wires) and the red probe of the meter to each of the three contacts for the stator. Record the numbers. Then swap around the meter leads (red and black are swapped) and take the readings again. You have thus measured the ground side of the rectifier.
If you have lower resistance in both directions (5+ ohms) then it's shot. If you have infinite in both directions, then it's shot. Throw it away.
Do not buy a Suzuki rectifier. I have purchased my replacement rectifiers off Ebay fro the last six or seven years and haven't had an issue with any of them. I've purchased them all from domestic suppliers that make them for a plethora of motorcycles, ATV's and dirtbikes. You will find them by searching. I have only purchased domestic. These rectifiers have not given me a bit of issue. I have one on my son's track bike (2005 GSXR 600) since 2008 and that thing get's beat hard in the summer from 7000 RPM to redline over and over all day. The cost is about 20% cheaper than OEM from Suzuki.
Hope this was helpful