Getting a lot of rain in California currently, and I drove through a flooded road. I could still see the sidewalk under the water, but it was still deep and admittedly stupid of me.

I checked my air filter immediately after crossing, it was dry and so was the tube leading into it (the part that is visible). And everything behaved normally on the 5 mile drive home. No misfires, CEL, or strange noises.

But I'm a little afraid of my rear diff took in water, I haven't done the breather mod yet. And my oil pan gasket is leaky, should I worry about water getting into the engine oil? I took the oil cap off and didn't see any steam.

Are there any other fluids or electrical connectors I should check, swap, or drain? Should I definitely drain my rear diff fluid?

sorry if this was asked

Pretty good chance you got some water in your rear diff, I’d drain and refill then not worry about it. Any minor amount of water that may have gotten in through a leaky oil pan gasket will evaporate off when your engine is at operating temp, though I doubt any got in.

I got water in my rear diff doing the same thing, it’s fine and still going strong in another 4Runner

+1 on checking the rear diff for sure, as you will want to drain and fill it with fresh fluid. It's also a good time to replace the breather, whether you want to do the extension mod or not. It can be swapped in under 60 seconds. I have the OEM p/n if you want it. I don't have the p/n for the extended one, but I'm sure it's easy to find.

Okay I'll definitely change the fluid. Are there any connectors I should look at? Don't want green death.

Agree with the other posters assessments.
Wouldn't hurt to grease the various propeller (AKA 'drive') shaft zirc fittings. Toyota (in the FSMs) sez to regrease prop shaft after being submerged in water.
Depending on how long they were submerged, the wheel bearings could take a hit from water.

If that's what you drove through I wouldn't worry about it.
You could remove the fill plug on the rear diff and see what the oil looks like.
If it looks like oil then it's ok. If it looks like chocolate milkshake then change it.

You don't have to worry about water getting into your oil pan.
As far as other things, they get wet when you go through puddles.

No need to worry about the bearings. It is seald and have grease seals. I drove my Corolla (1992) through a flooded road where water was half way at the door and flood the interior touching my gas paddle... I am shocked to see the engine was running all the way... At once, water came over the hood and the wave reached the wipers. Had some water inside the air box, but not to the point to wet the filter!

Thanks everyone. I've already replaced the diff oil now because it wasn't new fluid anyway.

There was no water in it, which is surprising because water got quite high (above the hubs for sure). And I knew where the air intake was located and in my opinion it got too close for comfort.

I'll grease the zerks tomorrow, I was planning to do that before I went back to Washington anyway. The diff breather extension is on my to do list now.

If it didn't break over the hood and nothing is in the axle I wouldn't think twice over it. But that said I wouldn't get comfortable doing it; these cars are made like swiss cheese and NOT meant for fording whatsoever
To a degree it baffles me how people create an "off road capable" vehicle without floor drains like Jeep... especially when we have things like ABS and diff lock ECUs mounted in low corners of the cab that will certainly pool water first

It's not as bad as the 2nd Gen 4Runners. The ECU was placed in a kick panel right next to the door. Guess where water normally comes in? THE DOOR!!

So many guys would soak their ECUs and then the engine would randomly cut out and throw a host of random codes.

There are floor drains right below the carpet. Most NGO's request a plastic carpeted 4x4's with a raised air intake for this reason.