On 4Runners and most Toyota trucks this isn't an issue; the stock fan our vehicles is a clutch fan. The clutch will allow some slip once it's in water so that it won't be damaged or force any of the blades into the radiator. As long as you don't venture too deep for extended periods you'll be fine or else you run the risk of overheating the fan.
One other thing no one has mentioned. If you have to cross water deep enough to submerge your fan, either go VERRRRRY slow or disconnect it (remove the belt or if electric, disconnect the wires) or risk deflecting the fan into the radiator with traumatic results. Yes, I know it can happen (thank goodness not to me). On my old Suburban that we use on the farm and off-road I put on an electric fan with a switch in the cab (also routed vent hoses with care, raised the intake to the cowl vent, and moved the computer and fuse block as high as possible),