Stock a 4Runner can run in water up to the top of the tires with minimal risk to ingesting water into the intake (pop your hood and the air filter box open and see where the intake draws air from the passenger side fender). When doing water crossings with a 4Runner, be sure to let your differentials/transmission/etc. cool by letting the vehicle idle a few minutes before entering the water. The water temperature can cause the oil/fluids of the systems to shrink due to thermal expansion/contraction (I was in the pool!), and there are one-way check valves that when submerged in water go closed. This can pull a slight vacuum on seals and can cause them to leak if there is too great of a deltaT.
Have you seen a dirt problem in your intake downstream of the air filter? If not, then you're good as is (hint, that's what air filters are for).
If you're doing water crossings 'hot' (desert sprints and then crashing into water crossings), then think about extending the 'one-way check valves' into high point 'breathers'.
If you're doing water crossings above the top of the tires, then think about a boat.