I once asked a question about restarting a flooded car for the first time. The well-reasoned opinion in the thread was to at least drain the water out of the gearbox before even starting it, let alone running it. The the gear oil will float on the water. The water from the bottom will be sloshing around on the gears doing most of the lubricating, which it won’t do well. The water will promote corrosion in parts that aren’t ordinarily exposed to water. I would say, at the very least, get it on jack stands, let the water settle into the bottom of the gearbox, then drain until clean oil starts flowing out. Quickly recap it, and top it off with clean gear oil. If you didn’t let too much gear out oil when draining the water, you might be able to get away briefly with driving it slightly low on gear oil but I wouldn’t push my luck on that. Transmissions use a lot less oil than engines, so even a small loss of oil could be significant. Good luck.