I get a lot of mail about ways to waterproof an off-road vehicle's electrical system. The only truly waterproof engines that I know of are those built with fording kits and developed for the military. However, with a little extra effort, we can at least improve the situation to tolerate something in between running in a damp fog and total submersion.
First, start with quality electrical components that are in excellent condition. This includes all primary and secondary ignition wiring, cap and coil. Over the past few years, vehicle manufacturers have actually done a darn good job of sealing up the wires, but that doesn't mean that there can't be improvements. The spark plug wiring should have a long, tight-fitting molded boot on the spark plug end, and the distributor nipple should also fit tightly. Holding these nipples even tighter to the cap with small nylon ties isn't a bad idea.
Before installation, the insides of all connectors, both primary and secondary, should be covered with dielectric grease or at a minimum be sprayed with a moisture repellant such as WD-40. If the nipples or boots don't appear to be completely sealed at the wire entrance, use either weatherstripping adhesive or RTV sealant.
Keeping water out of the distributor is important. The distributor can collect oil vapors and condensation from the engine itself, and must not remain completely sealed for any length of time. My preference is to seal the base of the cap and all wire openings with soft, non-hardening putty. On the side away from the radiator, I drill a 1/4-inch hole in a non-critical area of the distributor cap. When I know I'll encounter wet conditions, I just cover this hole with a piece of tape and then hope I can remember to remove it.
Another neat trick is to "T" off a manifold vacuum line and hook up a vacuum hose to the distributor cap. Depending on the size of hose used, you may be able to push the hose directly into the cap's drilled hole, or it may be necessary to epoxy a fitting in place. Either way, in theory, this vacuum keeps the distributor clean and dry. However, it is a fine line between just what is the correct amount of vacuum to be pulled. A small valve found in aquarium stores will allow you to control the air flow.
But what about the starter and alternator? Don't worry about the starter-unless the engine dies in midstream. If you have encountered deep water, just remember not to turn off the engine until radiated and transferred heat has done what it can to dry out the starter. The starter is primarily a sealed unit, and very little water will get into it. However, residual dirt that accompanies water can bind up the starter.
The alternator is a different story. You don't want to totally submerge it if at all possible. On some vehicles, the alternator is mounted down low and sometimes can be relocated with an aftermarket kit.
Making a charge through deep water such as a stream crossing may look cool on a magazine cover but is not really a good idea. The forced water can be driven into places you really don't want it to be in. Just recently, a friend charged through a water crossing, and when exiting, experienced a severe engine vibration. A close inspection under the hood revealed that one of the fan blades was missing. When the fan hit the wall of water, there was sudden stoppage and the blade actually sheared off from the fan hub.
One way to help avoid drowning the engine when crossing deep water is to disconnect the fan. That's a great idea if you have about three hours to pull the radiator, unbolt the fan, bolt the pulley back on again, and replace the radiator. Those with electric fans can simply disconnect the electrical plug right at the fan or, even better if some forethought is involved, place a switch in the electrical line to the fan. Another choice is to simply take off the fan belt. However, you'll not only stop the fan but you'll stop the water pump from circulating cooling water throughout the engine. An engine already at the 205-degree mark doesn't take long to get really hot, so only use this method if the crossing is short.
A better choice is to leave the fan on, but put your floor mat between the radiator and grille. Now, when you drive through the water, maintain a reasonable, steady speed. The vehicle's bow wave will keep most of the water out of the engine compartment, and the floor mat will keep any from entering through the radiator.
Some vehicles are prone to sucking up water with their air intakes. The fix may be as simple as disconnecting the pick-up ducting at the grille and redirecting it to the rear. A piece of foam rubber in the intake, a nylon stocking, or even a shop rag stretched across the opening will help keep the water out, but don't forget to remove them later because they all restrict a lot of air. I try to avoid deep water crossings, but I do take the precaution of using a foam pre-filter around the open-element K&N filter that I use. The oil gauze that makes up the K&N filter (www.knfilters.com) is also much better at resisting water intake than a paper filter element. ARB (www.arbusa.com) offers a great snorkel kit that pulls fresh air above the roof line.
What about the rest of the drivetrain-the front and rear differentials, the transmission, and the transfer case? All of these have vents. Some from the factory have short hoses, or no hoses, with the vent mounted on the axletube. All of the vents should have long hoses hooked to them and raised well above the deepest water you expect to encounter and away from where dust and water can collect. In some instances, one can use a small K&N filter on the end of the hose. If you can't get it higher than any water that you may have to drive through, the hose ends should use a one-way check valve.
One of the nicest vent setups I've come across is from North East Xtreme Tech (www.northeastxt.com). These come in a single-hose model or those that will take three lines. These are CNC-machined of billet aluminum and come with mounting hardware.
The possibility exists that water is going to get in and mix with the lubricants, especially at the axlehousing. Seals are designed to keep a lubricant in; they do a pretty good job of keeping trash out, but they are not foolproof. Hitting a big water hole on the trail means an instant cooldown of the axlehousing. When it cools, it tries to draw in air. This negative pressure is usually handled by the vent and breather, but if there is water pressure pushing on the axle seal, water can be drawn in. After prolonged water crossing, draining and refilling everything with fresh lubricants-engine included-is wise..